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Mass-spectrometry assisted heavy-atom derivative screening of human Fc gamma RIII crystals. | s; these heavy-atom compounds were also used to soak crystals of Fc gamma RIII and crystallographic data were collected after soaking. The calculated R(iso) indicated that HgCl(2); TMLA; K(2)PtCl(4) and PbAc(2) were likely to form derivatives; whereas KAu(CN)(2) and Na(2)WO(4) were not. The anomalous difference Patterson maps calculated for the HgCl(2) and TMLA derivative data sets were of good quality and can readily be interpreted by hand. In general; the number of binding sites obtained from the crystall | 10666595 | [
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Mass-spectrometry assisted heavy-atom derivative screening of human Fc gamma RIII crystals. | ographic phase refinement of the derivatives agrees with those obtained from the mass spectrometry; suggesting that mass spectrometry can be applied for rapid searching of suitable heavy-atom derivatives for X-ray crystallography. | 10666595 | [
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A stochastic approach to molecular replacement. | The classical approach to the problem of placing n copies of a search model in the asymmetric unit of a target crystal structure is to divide this 6n-dimensional optimization problem into a succession of three-dimensional searches (rotation-function followed by translation-function searches for each of the models). Here; it is shown that a structure-determination method based on a reverse Monte Carlo minimization of a suitably chosen statistic in the 6n-dimensional space defined by the rotational and transl | 10666596 | [
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A stochastic approach to molecular replacement. | ational parameters of the n molecules is both feasible and practical; at least for small n. Because all parameters of all molecules are determined simultaneously; this algorithm is expected to improve the signal-to-noise ratio in difficult cases involving high crystallographic/non-crystallographic symmetry in tightly packed crystal forms. Preliminary results from the application of this method (obtained with a space-group general computer program which has been developed for this purpose) are presented. | 10666596 | [
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A rational approach towards successful crystallization and crystal treatment of human cytomegalovirus protease and its inhibitor complex. | The crystallization and subsequent crystal treatment of both free human cytomegalovirus (hCMV) protease and its inhibitor complexes are reported. For free-enzyme crystals; diffraction was greatly improved by optimizing the crystallization conditions; raising the precipitant concentration in the reservoir and soaking the crystals in artificial mother liquors. Each of the six components in the final crystallization formula (16% PEG 4000; 0.1 M MES pH 6.0; 0.4 M LiCl; 10% glycerol; 5% t-butanol and 5 mM Na(2)S | 10666597 | [
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A rational approach towards successful crystallization and crystal treatment of human cytomegalovirus protease and its inhibitor complex. | (2)O(3)) plays a distinctive role and is indispensable. A synergistic effect of Na(2)SO(4) and t--butanol on diffraction was observed and studied. A 2.0 A multiwavelength anomalous diffraction (MAD) data set was collected using a synchrotron-radiation source; leading to the elucidation of the three-dimensional structure of the enzyme. For the inhibitor-complex crystals; initial attempts with co-crystallization and soaking experiments at pH 6.0 did not produce conclusive results. Subsequently; experiments we | 10666597 | [
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A rational approach towards successful crystallization and crystal treatment of human cytomegalovirus protease and its inhibitor complex. | re designed to co-crystallize the complex at pH 8.0; the optimal pH for the enzyme and the inhibitor activity. Using 20-50 mM spermine in the crystallization buffer; crystals of two peptidomimetic inhibitor complexes were obtained at pH 7.5 and 8.0. Spermine was required for the inhibitor complexes to be crystallized at pH 8.0; possibly neutralizing net negative charges of hCMV protease owing to its acidic pI of 5.5. A 2.7 A data set was collected from one of the inhibitor complexes and the structure was de | 10666597 | [
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Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. | Xylanases (1;4-beta-D-xylan xylanhydrolases; E.C. 3.2.1.8) hydrolyze the 1;4-beta-D-xylopyranosyl linkage of xylans. The structural characterization of xylanase active sites is of great interest; since it can lead to a better understanding of their catalytic mechanism and contribute significant knowledge to the rational design of specific oligosaccharide-binding sites via protein engineering. An intracellular xylanase gene (xynA2) from Bacillus stearothermophilus T-6 has recently been cloned and sequenced. | 10666598 | [
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Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. | The xynA2 gene encodes for an intracellular enzyme (IXT6) of 331 amino acids; with a calculated molecular weight of 38 639 Da and a pI of 5.72. Based on sequence homology; the enzyme belongs to family 10 of the glycosyl hydrolases. The xynA2 gene product (IXT6) was overproduced in Escherichia coli and purified to homogeneity. Crystallographic studies of IXT6 were initiated in order to study the specificity and mechanism of catalysis of this unique xylanase; as well as to provide a structural basis for ratio | 10666598 | [
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Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. | nal introduction of enhanced thermostability by site-specific mutagenesis. The M1 crystal form was found to be the most suitable for detailed crystal structure analysis. These crystals belong to a C--centered monoclinic crystal system (space group C2) with unit-cell parameters a = 170.6; b = 82.5; c = 80.0 A; beta = 91.43 degrees. They are mechanically strong; are fairly stable in the X-ray beam and diffract X--rays to better than 2.5 A resolution. A full 2.9 A resolution diffraction data set (97.9% complet | 10666598 | [
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Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. | eness; R(merge) = 8.4%) has recently been collected from one crystal at room temperature using X-ray synchrotron radiation (lambda = 1.125 A) and a MAR300 imaging-plate area detector. A comparable 2.5 A data set was measured at 90 K using a rotating-anode X-ray source and an R-AXIS IIc imaging-plate area detector (97.2% completeness; R(merge) = 6.9%). Molecular-replacement studies and multiple anomalous dispersion (MAD) experiments are currently in progress in order to determine the detailed three-dimension | 10666598 | [
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Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. | al structure of IXT6. | 10666598 | [
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Crystallization and preliminary X-ray analysis of luffaculin, a ribosome-inactivating protein from sponge-gourd seeds. | Luffaculin is a ribosome-inactivating protein. Crystals suitable for X--ray diffraction were first obtained using the hanging-drop vapour-diffusion method. X-ray studies show that the crystals belong to space group C2; with unit-cell parameters a = 89.90; b = 59.82; c = 55.18 A; beta = 120.81 degrees; and have one molecule in the crystallographic asymmetric unit. The crystals diffract X-rays to at least 2.0 A resolution. | 10666599 | [
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Crystallization and preliminary X-ray crystallographic analysis of the 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes. | The 30 kDa membrane-binding domain of protein 4.1 from human erythrocytes has been expressed in Escherichia coli and crystallized in a form suitable for X-ray crystallographic study. Crystals were grown using a salting-in technique. Crystals have a tetragonal plate shape and belong to the C2 space group; with unit-cell parameters a = 163.9; b = 106.5; c = 93.5 A; beta = 95.5 degrees. The crystals diffract to 2.8 A resolution. | 10666600 | [
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Crystallization and preliminary X-ray diffraction analysis of human calcium-binding protein S100A12. | S100A12; a member of the calgranulin family; isolated from human blood; has been crystallized by vapour diffusion in the presence of Ca(2+). Crystals belong to the space group R3 with unit-cell dimensions a = b = 99.6 c = 64.2 A. There are two monomers per asymmetric unit; with a solvent content of 57.9%. The crystals diffract to at least 2.2 A resolution and complete X-ray data have been collected to 2.5 A on a conventional laboratory source. | 10666601 | [
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Crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of ADP-glucose pyrophosphorylase from potato tuber. | ADP-glucose pyrophosphorylase is the key regulatory enzyme in the biosynthesis of starch in plants and glycogen in bacteria. The enzyme from potato tuber is comprised of a regulatory subunit and a catalytic subunit and is present as a heterotetramer (alpha(2)beta(2)). The catalytic subunit from potato tuber (50 kDa) was crystallized in four different forms; two of which are suitable for structural studies. A tetragonal crystal form obtained in the presence of the substrate analog Cr-ATP diffracted to 2.2 A | 10666602 | [
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Crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of ADP-glucose pyrophosphorylase from potato tuber. | and belongs to space group P4(1) (or its enantiomorph); with unit-cell parameters a = b = 110.57; c = 190.14 A. A second crystal form obtained diffracted to 2.8 A and belongs to space group P2; with unit-cell parameters a = 80.06; b = 138.84; c = 92.20 A; beta = 112. 40 degrees. As this protein displays no significant homology to any currently known protein structure; a search for heavy-atom derivatives has been initiated. | 10666602 | [
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Crystallization and preliminary X-ray diffraction analysis of Thermus thermophilus prolyl-tRNA synthetase. | Prolyl-tRNA synthetase from Thermus thermophilus (ProRSTT) was purified to homogeneity using a five-step purification procedure and was crystallized using ethylene glycol as a precipitant. Crystals of ProRSTT belong to the space group P2(1)2(1)2; with unit-cell parameters a = 132; b = 191; c = 125 A; have two homodimers per asymmetric unit and diffract to 2.4 A resolution. A complete native data set to 2.43 A resolution has been collected and a data set from ProRSTT in complex with proline has been collecte | 10666603 | [
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Crystallization and preliminary X-ray diffraction analysis of Thermus thermophilus prolyl-tRNA synthetase. | d to 2.9 A resolution. | 10666603 | [
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Improved crystals of Thermus thermophilus prolyl-tRNA synthetase complexed with cognate tRNA obtained by crystallization from precipitate. | The complex between Thermus thermophilus prolyl-tRNA synthetase (ProRSTT) and its cognate tRNA has been crystallized using two different isoacceptors of tRNA(Pro). Similar bipyramidal crystals of the complexes of ProRSTT with the two different tRNA(Pro) isoacceptors grow within two weeks from 32% saturated ammonium sulfate solution. They belong to space group P4(3)2(1)2; with unit-cell parameters a = 143.1; b = 143.1; c = 228.6 A. The crystals diffract weakly to a maximum resolution of 3.1 A. Superior quali | 10666604 | [
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Improved crystals of Thermus thermophilus prolyl-tRNA synthetase complexed with cognate tRNA obtained by crystallization from precipitate. | ty crystals were obtained by growing slowly from precipitate over 5-6 months. These are of the same space group but have slightly altered unit-cell parameters; a = 140.8; b = 140.8; c = 237.0 A. These crystals diffract more strongly to at least 2.8 A resolution and a complete data set to 2.85 A resolution has been collected from a single crystal. Comparison of the packing in the two crystal forms shows that domain flexibility contributes to the presence of different crystal contacts in the two forms. | 10666604 | [
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Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus. | A recombinant alpha-amylase from Bacillus stearothermophilus was found to be produced as several isoforms arising from different N--terminal processing. Some of those isoforms were purified to homogeneity and crystallized at 293 K using the hanging-drop vapour-diffusion method under the following conditions: 35 mM sodium acetate (pH 4.6); 6.25%(v/v) 2-propanol; in the presence of 1.23%(w/v) acarbose (a pseudo-oligosaccharide inhibitor) in the drop. The crystals diffracted beyond 2.0 A resolution using synch | 10666605 | [
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Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus. | rotron radiation at the Photon Factory; Tsukuba. They belong to the monoclinic space group P2(1); with unit-cell parameters a = 53.7 (2); b = 92.9 (4); c = 53.2 (2) A; beta = 109.4 (1) degrees. | 10666605 | [
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Crystallization and preliminary X-ray studies of recombinant amylosucrase from Neisseria polysaccharea. | Recombinant amylosucrase from Neisseria polysaccharea was crystallized by the vapour-diffusion procedure in the presence of polyethylene glycol 6000. The crystals belong to the orthorhombic space group P2(1)2(1)2; with unit-cell parameters a = 95.7; b = 117.2; c = 62.1 A; and diffract to 1.6 A resolution. A p-chloromercuribenzene sulfonate (pcmbs) derivative has been identified and a selenomethionine-substituted protein has been produced and crystallized. | 10666606 | [
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Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase. | Phosphonoacetaldehyde hydrolase; a C-P bond-cleaving enzyme which utilizes an unusual bicovalent catalytic strategy; has been crystallized by the hanging-drop vapor-diffusion method using PEG 4000 as the precipitant. The crystals belong to the monoclinic system and belong to space group C2; with unit-cell parameters a = 210.5; b = 45.5; c = 64.7 A; beta = 105.0 degrees. The asymmetric unit contains a dimer related by a non-crystallographic dyad. In addition to a 2.7 A native data set; the following data set | 10666607 | [
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Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase. | s have been collected: a 2.4 A data set from crystals complexed with the intermediate analog vinyl sulfonate; a 3.0 A three-wavelength MAD data set from crystals complexed with the product analog WO(4)(2-); as well as several heavy-atom data sets to 3.0 A or better; of which only three have proven useful for MIR calculations. Examination of the native Patterson map revealed NCS that made previously uninterpretable derivative data useful. Independent phase sets were first calculated and refined for the MAD a | 10666607 | [
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Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase. | nd MIR experiments separately and were then combined. The combined phase set was further improved by solvent flattening; histogram matching and NCS averaging. Interpretation of the resulting electron-density map is currently under way. | 10666607 | [
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Crystallization and preliminary X-ray diffraction studies of a beta-carbonic anhydrase from the red alga Porphyridium purpureum. | The beta-carbonic anhydrase from the red alga Porphyridium purpureum was heterologously expressed; purified and crystallized. The crystals belong to space group P2(1) (unit-cell parameters a = 63.8; b = 113.9; c = 73.8 A; beta = 104.1 degrees) with two subunits per asymmetric unit and diffract to 2.5 A resolution. | 10666608 | [
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Expression, crystallization and preliminary X-ray studies of the PDZ domain of Dishevelled protein. | Dishevelled (Dsh) protein is an important component of the Wnt signal-transduction pathway. It has three relatively conserved domains: DIX; PDZ and DEP. The PDZ domain of the Xenopus laevis homolog of Dsh; which consists of residues 254-348; was overexpressed as a soluble protein in Escherichia coli; purified and crystallized. The crystals were obtained by the vapor-diffusion method; using 1.4 M sodium formate as a precipitant. The crystals diffracted to 2.3 A resolution. The space group was determined to b | 10666609 | [
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] |
Expression, crystallization and preliminary X-ray studies of the PDZ domain of Dishevelled protein. | e P6(1)22 or P6(5)22; with unit-cell dimensions a = b = 95.9; c = 93.9 A. | 10666609 | [
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Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. | Nitrite reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is a multihaem (type c) membrane-bound enzyme that catalyzes the dissimilatory conversion of nitrite to ammonia. Crystals of the oxidized form of this enzyme were obtained using PEG and CaCl(2) as precipitants in the presence of 3--(decylmethylammonium)propane-1-sulfonate and belong to the space group P2(1)2(1)2(1); with unit-cell parameters a = 78.94; b = 104.59; c = 143.18 A. A complete data set to 2.30 A resoluti | 10666610 | [
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Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. | on was collected using synchrotron radiation at the ESRF. However; the crystals may diffract to beyond 1.7 A and high-resolution data will be collected in the near future. | 10666610 | [
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X-ray studies of recombinant anti-testosterone Fab fragments: the use of PEG 3350 in crystallization. | Recombinant anti-testosterone wild-type Fab fragment and mutant Fab fragments with high binding selectivity developed by protein engineering have been crystallized with and without ligands. Crystals of these Fab fragments were obtained by the vapour-diffusion technique at room temperature using solutions of PEG 3350 with various biological buffers and with a wide pH range. So far; five data sets have been collected from crystals of three Fab-antigen complexes and from two uncomplexed Fab fragments; with res | 10666611 | [
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X-ray studies of recombinant anti-testosterone Fab fragments: the use of PEG 3350 in crystallization. | olutions ranging from 2.10 to 3.1 A. Crystallization conditions for Fab fragments were found by using modifications of the low ionic strength PEG 3350 series. Suitable concentrations of PEG 400; MPD and glycerol solutions for use as cryoprotectants in PEG 3350 solutions have been determined. One useful observation was that PEG 3350 is able to work alone as a cryoprotectant. The screening protocol used requires a smaller amount of protein material to achieve auspicious pre-crystals than previously. Results s | 10666611 | [
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X-ray studies of recombinant anti-testosterone Fab fragments: the use of PEG 3350 in crystallization. | upport the claim that PEG 3350 is more suitable for the crystallization of Fab fragments than higher molecular weight PEGs. | 10666611 | [
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Crystallization and preliminary X-ray analysis of the thymidylate kinase from Mycobacterium tuberculosis. | Mycobacterium tuberculosis thymidylate kinase complexed with the substrate deoxythymidine monophosphate was crystallized in the hexagonal space group P6(5)22 or P6(1)22; with unit-cell parameters a = b = 76.62; c = 134.38 A and one single monomer of 23 kDa in the asymmetric unit. Cryo-cooled crystals diffract at 1.94 A resolution using synchrotron radiation. | 10666613 | [
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Crystallization and preliminary X-ray diffraction analysis of the Saccharomyces cerevisiae ran-binding protein Mog1p. | Mog1p binds the Ras-family GTPase Ran/Gsp1p; which has a central role in nucleocytoplasmic transport and cell-cycle progression. Overexpression of MOG1 is able to suppress temperature-sensitive gsp1 mutants in yeast; Deltamog1 null mutants display temperature-sensitive defects in nuclear trafficking. Orthorhombic crystals of bacterially expressed Mog1p that diffract to beyond 2 A resolution using synchrotron radiation have been obtained. The crystals have P2(1)2(1)2(1) symmetry; with unit-cell parameters a | 10666614 | [
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Crystallization and preliminary X-ray diffraction analysis of the Saccharomyces cerevisiae ran-binding protein Mog1p. | = 39.67; b = 51.96; c = 112.23 A; a Matthews coefficient of 2.44 A(3) Da(-1); an estimated solvent content of 49.5% and one chain in the asymmetric unit. | 10666614 | [
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The purification, crystallization and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar typhimurium. | dTDP-D-glucose 4;6-dehydratase (RmlB) is the second of four enzymes involved in the dTDP-L-rhamnose pathway and catalyzes the dehydration of dTDP-D-glucose to dTDP-4-keto-6-deoxy-D-glucose. The ultimate product of the pathway; dTDP-L-rhamnose; is the precursor of L-rhamnose; which is a key component of the cell wall of many pathogenic bacteria. RmlB from Salmonella enterica serovar Typhimurium has been overexpressed and purified; and crystals of the enzyme have been grown using the sitting-drop vapour-diffu | 10666612 | [
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The purification, crystallization and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar typhimurium. | sion technique with lithium sulfate as precipitant. Diffraction data have been obtained to a resolution of 2.8 A on a single frozen RmlB crystal which belongs to space group P2(1); with unit-cell parameters a = 111.85; b = 87.77; c = 145.66 A; beta = 131.53 degrees. The asymmetric unit contains four monomers in the form of two RmlB dimers with a solvent content of 62%. A molecular-replacement solution has been obtained and the model is currently being refined. | 10666612 | [
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Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. | A quick (less than 1 min) soak of protein crystals in a cryo-solution containing bromide or iodide anions leads to incorporation of these anomalous scatterers into the ordered solvent region around the protein molecules. These halide anions provide a convenient way of phasing through their anomalous scattering signal: bromides using multiwavelength anomalous dispersion (MAD) and bromides and/or iodides using single-wavelength anomalous dispersion (SAD) or single isomorphous replacement with anomalous scatte | 10666615 | [
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Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. | ring (SIRAS) methods. This approach has been tested successfully on four different proteins and has been used to solve the structure of a new protein of molecular weight 30 kDa. | 10666615 | [
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P1 Shake-and-Bake: can success be guaranteed? | The multi-trial direct-methods procedure known as Shake-and-Bake has been applied to three small proteins (alpha-1 peptide; vancomycin and lysozyme) that crystallize in space group P1. Phase refinement was accomplished through parameter-shift optimization using both the cosine and exponential forms of the minimal function. By extending error-free data to sufficiently high resolution; 100% convergence of trial structures to solution could be achieved in all three cases by using the exponential minimal functi | 10666616 | [
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P1 Shake-and-Bake: can success be guaranteed? | on and a shift angle in the range 130-150 degrees. These results suggest optimum parameters for other P1 structures and emphasize the importance of collecting data to the highest possible resolution. | 10666616 | [
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] |
Structure of human erythrocyte catalase. | Catalase (E.C. 1.11.1.6) was purified from human erythrocytes and crystallized in three different forms: orthorhombic; hexagonal and tetragonal. The structure of the orthorhombic crystal form of human erythrocyte catalase (HEC); with space group P2(1)2(1)2(1) and unit-cell parameters a = 84.9; b = 141.7; c = 232.5 A; was determined and refined with 2.75 A resolution data. Non-crystallographic symmetry restraints were employed and the resulting R value and R(free) were 0.206 and 0.272; respectively. The over | 10666617 | [
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] |
Structure of human erythrocyte catalase. | all structure and arrangement of HEC molecules in the orthorhombic unit cell were very similar to those of bovine liver catalase (BLC). However; no NADPH was observed in the HEC crystal and a water was bound to the active-site residue His75. Conserved lattice interactions suggested a common growth mechanism for the orthorhombic crystals of HEC and BLC. | 10666617 | [
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A preliminary neutron Laue diffraction study of the aspartic proteinase endothiapepsin. | Until now; no aspartic proteinase has been subjected to a successful neutron diffraction analysis; owing to the limited size of the crystals. However; the recent development of the neutron Laue technique at ILL and EMBL (Grenoble) has allowed the collection of data to 2.2 A on a complex of endothiapepsin with a transition-state analogue. The objective is to define the positions of the protons at the active site by refinement using the neutron data. In line with work on serine proteinases; where neutron diff | 10666618 | [
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A preliminary neutron Laue diffraction study of the aspartic proteinase endothiapepsin. | raction has provided some of the most definitive data on the catalytic mechanism; it is expected that this work will have a major significance for studies of the aspartic proteinase enzymes. | 10666618 | [
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Biological crystallography goes online | nan | 10666619 | [
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] |
The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. | The structure of bovine interferon-gamma (IFN-gamma) was determined by multiple isomorphous replacement at 2.0 A resolution. Bovine IFN-gamma crystallizes in two related crystal forms. Crystal form 1 diffracts to 2.9 A resolution and is reproducible and stable to derivatization. Crystal form 2 diffracts to 2.0 A resolution; but shows significant non-isomorphism from crystal to crystal. The previously determined structures of several different species of INF-gamma were either at too low a resolution [human; | 10666622 | [
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The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. | 1hig; Ealick et al. (1991); Science; 252; 698-702] or were too inaccurate [bovine; 1rfb; Samudzi & Rubin (1993); Acta Cryst. D49(6); 505-512; rabbit; 2rig; Samudzi et al. (1991); J. Biol. Chem. 266(32); 21791-21797] for the structure to be solved by molecular replacement. The structure was solved in crystal form 1 using two derivatives produced by chemically modifying two free cysteine residues that were introduced by site-directed mutagenesis (Ser30Cys; Asn59Cys). After model building and refinement; the f | 10666622 | [
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The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. | inal R value was 21.8% (R(free) = 30.9%) for all data in the resolution range 8.0-2.9 A. The crystal form 1 structure was then used as a molecular-replacement model for crystal form 2 data collected from a flash-cooled crystal. Subsequent model building and refinement; using all data in the resolution range 15.0-2.0 A; gave an R value of 19.7% and an R(free) of 27.5%. Pairwise comparison of C(alpha) positions of bovine IFN-gamma (BOV) and the previously determined 1rfb and 2rig structures indicated some sig | 10666622 | [
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The 2.0 A structure of bovine interferon-gamma; assessment of the structural differences between species. | nificant differences in the models (r.m.s.d. values for BOV to 1rfb; 4.3 A; BOV to 2rig; 4.0 A). An assessment of the quality of the structures was made using the 3D-1D algorithm [Eisenberg et al. (1992); Faraday Discuss. 93; 25-34]. The resulting statistical scoring indicated that BOV was consistent with expected criteria for a 2.0 A structure; whereas both 1rfb and 2rig fell below acceptable criteria. | 10666622 | [
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Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A. | A new neurotoxin BmK M2; toxic to both mammals and insects; with the strongest toxicity in the BmK toxin series; has been purified from the Chinese scorpion Buthus martensii Karsch and crystallized with MPD at pH 7.5. The crystals are orthorhombic; belonging to space group P2(1)2(1)2(1); with unit-cell parameters a = 36.64; b = 36.95; c = 37.23 A. The structure was solved by molecular replacement and refined to R = 0.186 for all reflections to a resolution of 1.76 A. The whole sequence (64 residues) of BmK | 10666623 | [
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] |
Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A. | M2 was determined by crystallographic analysis based on high-resolution data and the homologous model of BmK M8. The refined BmK M2 structure shows a non-proline cis peptide bond between Pro9 and His10 which enables the C-terminal segment to adopt a conformation different to that of the weak toxin BmK M8. Recently; a mutation analysis had suggested that both the tenth residue and the C-terminus play key roles in receptor binding. Therefore; these features may be related to the binding selectivity of the gro | 10666623 | [
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] |
Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A. | up III alpha-like toxins. The charge changes of residues 8; 10; 18; 28; 55 and 59 from neutral or negative to positive or neutral; which leads to a positive electrostatic potential surface; may be responsible for the high toxicity of BmK M2. | 10666623 | [
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] |
The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5. | The crystal structure of the catalytic core domain of beta-mannanase from the fungus Trichoderma reesei has been determined at a resolution of 1.5 A. The structure was solved using the anomalous scattering from a single non-isomorphous platinum complex with two heavy-metal sites in space group P2(1). The map computed with the experimental phases was enhanced by the application of an automated model building and refinement procedure using the amplitudes and experimental phases as observations. This approach | 10666621 | [
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The three-dimensional structure of a Trichoderma reesei beta-mannanase from glycoside hydrolase family 5. | is expected to be of more general application. The structure of the native enzyme and complexes with Tris-HCl and mannobiose are also reported: the mannobiose binds in subsites +1 and +2. The structure is briefly compared with that of the homologous beta-mannanase from the bacterium Thermomonospora fusca. | 10666621 | [
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1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. | Abalone sperm use lysin to make a hole in the egg's protective vitelline envelope (VE). When released from sperm; lysin first binds to the VE receptor for lysin (VERL) then dissolves the VE by a non-enzymatic mechanism. The structures of the monomeric and dimeric forms of Haliotis rufescens (red abalone) lysin; previously solved at 1.90 and 2.75 A; respectively; have now been refined to 1.35 and 2.07 A; respectively. The monomeric form of lysin was refined using previously obtained crystallization condition | 10666624 | [
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1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. | s; while the dimer was solved in a new crystal form with four molecules (two dimers) per asymmetric unit. These high-resolution structures reveal alternate residue conformations; enabling a thorough analysis of the conserved residues contributing to the amphipathic nature of lysin. The availability of five independent high-resolution copies of lysin permits comparisons leading to insights on the local flexibility of lysin and alternative conformations of the hypervariable N-terminus; thought to be involved | 10666624 | [
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1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. | in species-specific receptor recognition. The new analysis led to the discovery of the basic nature of a cleft formed upon dimerization and a patch of basic residues in the dimer interface. Identification of these features was not possible at lower resolution. In light of this new information; a model explaining the binding of sperm lysin to egg VERL and the subsequent dissolution of the egg VE is proposed. | 10666624 | [
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RSPS version 4.0: a semi-interactive vector-search program for solving heavy-atom derivatives. | A program for inspection and interpretation of the Patterson function is described. The program is mainly intended for finding heavy-atom positions from difference Patterson maps; but may also be used to locate molecules with non-crystallographic symmetry when the local axis is nearly parallel to a crystallographic symmetry axis. Options are available for vector-based methods to locate heavy-atom sites; for finding sets from a list of possible heavy-atom positions and for checking of potential solutions. Bo | 10666625 | [
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Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data. | Neutron-diffraction data were collected from stacked bilayers of 1; 2-dioleoyl-sn-glycero-phosphocholine under conditions of increasing relative humidity at both 0 and 8.06% (2)H(2)O. Over the period of data collection; the d-repeat of both swelling-series samples increased. Each family of structure factors; representing each of the five orders of diffraction; are shown to lie on smooth curves; allowing structure factors of intermediate d-repeat to be determined. In the case of the 8.06% (2)H(2)O data; but | 10666626 | [
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Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data. | not the 0% (2)H(2)O data; all observed structure factors lie on a single continuous transform. 8.06% (2)H(2)O has a net neutron-scattering density of zero; its use in neutron-diffraction experiments presents a novel application of the so-called 'minus fluid' approach; without mathematical manipulation. The data are used to demonstrate the increased accuracy inherent in this real-time swelling-series approach. A quantitative analysis of errors caused by differences in d--repeat in difference subtractions is | 10666626 | [
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Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data. | presented. | 10666626 | [
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Effects of microgravity on the crystal quality of a collagen-like polypeptide. | (Pro-Pro-Gly)(10) is one of the most widely studied collagen polypeptide models. Microgravity crystal growth of (Pro-Pro-Gly)(10) was carried out in the Advanced Protein Crystallization Facility aboard the Space Shuttle Discovery during the STS-95 mission. Crystals were successfully grown in all experiments; using both dialysis and free-interface diffusion methods. The quality of the microgravity-grown crystals and of ground-grown counterparts was assessed by X-ray synchrotron diffraction. Microgravity-grow | 10666627 | [
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Effects of microgravity on the crystal quality of a collagen-like polypeptide. | n crystals exhibited a significant improvement in terms of dimensions and resolution limit. As previously reported; crystals were orthorhombic; space group P2(1)2(1)2(1). However; the diffraction pattern showed weak reflections; never previously measured; that were consistent with new unit-cell parameters a = 26.9; b = 26.4; c = 182.5 A. This allowed the derivation of a new model for the arrangement of the triple-helical molecules in the crystals. | 10666627 | [
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Crystallization and preliminary X-ray diffraction studies of human epidermal growth factor. | Human epidermal growth factor (hEGF); a 6.2 kDa protein of 53 amino acids with three internal disulfide bridges; has been crystallized by the hanging-drop method. hEGF crystallizes in space group P3(1)21 (or P3(2)21) using MgCl(2) as precipitant; with unit-cell parameters a = b = 61.4; c = 87.0 A. Another type of crystal; obtained using NaCl as precipitant; belongs to a tetragonal point group and has unit-cell dimensions a = b = 102.5; c = 166.6 A. The trigonal crystals with the smaller unit cell diffract X | 10666628 | [
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Crystallization and preliminary X-ray diffraction studies of human epidermal growth factor. | -rays better and a native data set from a single crystal has been collected to 3.0 A resolution. | 10666628 | [
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Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis. | N-utilizing substance B (NusB) is a protein which forms part of a complex assembly in transcriptional antitermination in Mycobacterium tuberculosis. It forms a heterodimer with the product of the NusE gene (identical to the ribosomal protein S10) and mediates the process of transcriptional antitermination by forming the core complex with the nut site of the ribosomal RNA along with other protein factors. NusB has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapou | 10666629 | [
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Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis. | r-diffusion method. The space group is P2(1)2(1)2(1); with unit-cell parameters a = 46.6; b = 64.2; c = 90.1 A. A native data set complete to 1.6 A resolution has been collected from a single crystal. | 10666629 | [
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Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site. | The catabolite control protein (CcpA) from Bacillus megaterium is a member of the bacterial repressor protein family GalR/LacI. CcpA with an N-terminal His-tag was used for crystallization. Crystals of free CcpA and of CcpA in complex with the putative operator sequence (catabolite responsive elements; CRE) were obtained by vapour-diffusion techniques at 291 K using the hanging-drop method. CcpA crystals grown in the presence of polyethylene glycol 8000 belong to the hexagonal space group P6(1)22 or P6(5)22 | 10666630 | [
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Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site. | ; with unit-cell parameters a = 74.4; c = 238.8 A. These crystals diffract X-rays to 2.55 A resolution and contain one monomer of the homodimeric protein per asymmetric unit. Crystals of the CcpA-CRE complex were obtained with ammonium sulfate as precipitant and belong to the tetragonal space group I4(1)22; with unit-cell parameters a = 125; c = 400 A and one complex per asymmetric unit. Although these co-crystals grew to a sufficient size; X-ray diffraction was limited to 8 A resolution. | 10666630 | [
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Crystallization and preliminary diffraction studies of a truncated form of a novel protease from spores of Bacillus megaterium. | During germination of spores of Bacillus species; a novel protease termed GPR initiates the degradation of a group of small acid-soluble spore proteins which protect the dormant spore's DNA from damage. Trypsin digestion of the zymogen of B. megaterium GPR removes approximately 15 kDa from the C-terminal end of the 46 kDa zymogen subunit; leaving a 30 kDa subunit. Single crystals of this truncated form of GPR have been obtained by the vapor-diffusion method using PEG 4000 as a precipitating agent. The cryst | 10666631 | [
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Crystallization and preliminary diffraction studies of a truncated form of a novel protease from spores of Bacillus megaterium. | als belong to the monoclinic space group P2(1); with unit-cell parameters a = 67.99; b = 105.34; c = 108.63 A; beta = 95.68 degrees. The cryofrozen crystals diffract X-rays to about 3.3 A using synchrotron radiation. | 10666631 | [
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Crystallization and preliminary X-ray analysis of recombinant full-length human m-calpain. | m-Calpain constitutes the prototype of the superfamily of neutral calcium-activated cysteine proteinases. It is a heterodimer consisting of an 80 and a 30 kDa subunit. Recombinant full-length human m-calpain has been crystallized using macro-seeding techniques and vapour-diffusion methods. Two different monoclinic crystal forms (space group P2(1)) were obtained from a solution containing polyethylene glycol (M(W) = 10 000) as a precipitating agent. Complete data sets have been collected to 2.3 and 3.0 A res | 10666632 | [
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Crystallization and preliminary X-ray analysis of recombinant full-length human m-calpain. | olution using cryo-cooling conditions and synchrotron radiation. The unit-cell parameters are a = 64.86; b = 133.97; c = 78.00 A; beta = 102.43 degrees and a = 51.80; b = 171.36; c = 64.66 A; beta = 94.78 degrees; respectively. The V(m) values indicate that there is one heterodimer in each asymmetric unit. | 10666632 | [
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Toxoplasma gondii adenosine kinase: expression, purification, characterization, crystallization and preliminary crystallographic analysis. | The obligate intracellular protozoan parasite Toxoplasma gondii depends on the purine-salvage pathway for its purine supply. Unlike its mammalian hosts; T. gondii salvages purine precursors predominantly via adenosine kinase; the enzyme that phosphorylates adenosine to adenosine monophosphate (AMP). The cDNA encoding T. gondii adenosine kinase was subcloned and expressed in Escherichia coli. The recombinant protein was active in an in vitro enzyme assay over a broad pH range. It required a divalent cation f | 10666633 | [
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Toxoplasma gondii adenosine kinase: expression, purification, characterization, crystallization and preliminary crystallographic analysis. | or activity. The enzyme was inactivated by the addition of 1 microM mercuric chloride. The inactivation could be reversed by a reducing agent. The active recombinant protein was crystallized using sodium sulfate as precipitant at pH 8.0. The crystals diffract to 1.8 A and belong to the monoclinic space group P2(1); with unit-cell parameters a = 47.5; b = 68.9; c = 57.0 A; beta = 100.3 degrees. The calculated V(m) based on one molecule per asymmetric unit is 2.38 A(3) Da(-1). | 10666633 | [
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Crystallization and preliminary X-ray diffraction studies of cytochrome c6 from Porphyra yezoensis. | Cytochrome c(6) from the red alga Porphyra yezoensis has been purified and crystallized by the sitting-drop vapour-diffusion method. Two different crystal forms; tetragonal and orthorhombic; were obtained. The tetragonal crystals belong to space group P4(1)2(1)2 or P4(3)2(1)2; with unit-cell dimensions a = 49.33 (2); c = 83.70 (10) A. The orthorhombic crystals belong to space group P2(1)2(1)2(1); with unit-cell dimensions a = 46.74 (2); b = 49.42 (1); c = 37.11 (1) A. Absorption spectra of the crystals show | 10666634 | [
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Crystallization and preliminary crystallographic studies of ribosome recycling factor from Escherichia coli. | Ribosome recycling factor (RRF) catalyzes the disassembly of a termination complex during the final stage of protein synthesis. RRF from Escherichia coli has been crystallized with PEG 400 as precipitant at 287 K. The crystal belongs to the trigonal space group P3(1)21 (or P3(2)21); with unit-cell parameters a = b = 48.08; c = 141.67 A. Native data were collected from a frozen crystal to a resolution of 3.0 A on a Cu Kalpha rotating-anode X-ray source. | 10666636 | [
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Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus. | The NADP-dependent beta-keto acyl-carrier protein reductase (BKR) from Brassica napus has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol of average molecular weight 1500 as the precipitant. The crystals belong to the hexagonal space group P6(4)22; with unit-cell parameters a = b = 129. 9; c = 93.1 A; alpha = beta = 90; gamma = 120 degrees. Calculated values for V(m); the use of rotation and translation functions and consideration of the packing suggest that the asymm | 10666637 | [
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Crystallization of the NADP-dependent beta-keto acyl-carrier protein reductase from Brassica napus. | etric unit contains a monomer. The crystals diffract to beyond 2.8 A resolution and are more amenable to X-ray diffraction analysis than those reported previously for the Escherichia coli enzyme. The structure determination of B. napus BKR will provide important insights into the catalytic mechanism of the enzyme and into the evolution of the fatty-acid elongation cycle by comparisons with the other oxidoreductase of the pathway; enoyl acyl-carrier protein reductase (ENR). | 10666637 | [
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Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis. | L(+)-Lactate dehydrogenase (LDH) is a key enzyme in anaerobic metabolism which converts pyruvate to lactate. LDH from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized in two crystal forms at 297 K using 2-methyl-2;4-pentanediol as precipitant. Type I crystals grew rapidly and diffracted to at least 2.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 2.9 A have been collected from a native crystal. The type | 10666635 | [
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Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis. | I crystal is tetragonal; belonging to the space group P4(2)2(1)2; with unit-cell parameters a = b = 99.74; c = 170.00 A. The asymmetric unit contains two LDH subunits; with a corresponding crystal volume per protein mass (V(m)) of 3.05 A(3) Da(-1) and a solvent content of 59.7%. Type II crystals; which grew more slowly; diffracted to at least 1.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 1.9 A have been collected from a native crystal. The type II crystal is orthorhombic; | 10666635 | [
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Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis. | belonging to the space group P2(1)2(1)2; with unit-cell parameters a = 47.65; b = 125.10; c = 58.08 A. The asymmetric unit contains a single LDH subunit; with a corresponding crystal volume per protein mass (V(m)) of 2.50 A(3) Da(-1) and a solvent content of 50.8%. Therefore; the type II crystal is more suitable for high-resolution structure determination than the type I crystal. | 10666635 | [
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Crystallization and preliminary X-ray diffraction analysis of the NAD-dependent non--phosphorylating GAPDH of the hyperthermophilic archaeon Thermoproteus tenax. | Recombinant non-phosphorylating NAD(+)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN) of the hyperthermophilic crenarchaeote Thermoproteus tenax has been overexpressed; purified and crystallized using the hanging-drop vapour-diffusion technique. Crystals of different habits were obtained from several precipitant solutions (salts and polyethylene glycols). Preliminary X-ray analysis was performed with crystals grown in ammonium formate; which belonged to the primitive hexagonal space group P622; a | 10666638 | [
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Crystallization and preliminary X-ray diffraction analysis of the NAD-dependent non--phosphorylating GAPDH of the hyperthermophilic archaeon Thermoproteus tenax. | nd had unit-cell parameters a = b = 184.8; c = 133.0 A; gamma = 120 degrees. Assuming a molecular weight of 55 kDa; a Matthews parameter of 3.3 A(3) Da(-1) is calculated assuming two molecules per asymmetric unit. The diffraction limit of these crystals is 2.5 A resolution. | 10666638 | [
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Crystallization and preliminary X-ray analysis of the catalytic core of the alkylhydroperoxide reductase component AhpF from Escherichia coli. | Alkylhydroperoxide reductases (AhpR; E.C. 1.6.4.x) are essential for the oxygen tolerance of aerobic organisms; converting otherwise toxic hydroperoxides of lipids or nucleic acids to their corresponding alcohols. The AhpF component (521 amino-acid residues; 56.2 kDa) belongs to the family of pyridine nucleotide-disulfide oxidoreductases and channels electrons from NAD(P)H via a series of disulfides towards the AhpC component; which finally reduces the hydro-peroxide substrates. Crystals of the proteolytica | 10666639 | [
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Crystallization and preliminary X-ray analysis of the catalytic core of the alkylhydroperoxide reductase component AhpF from Escherichia coli. | lly truncated AhpF component (residues Asn208-Ala521) of the alkyl hydroperoxide reductase from Escherichia coli were grown under oxidizing conditions. The crystals belong to space group P3(2)21; with unit-cell parameters a = 60.4; c = 171.8 A. X-ray diffraction data were collected to 1.9 A resolution using synchrotron radiation. A molecular-replacement solution was found using the structure of thioredoxin reductase from Arabidopsis thaliana as a search model. | 10666639 | [
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Crystallization and preliminary X-ray analysis of a bacteriophage T4 primase fragment. | The primase from bacteriophage T4 is a single-stranded DNA-dependent RNA polymerase that is one of the seven proteins that constitute the DNA-replication machinery of bacteriophage T4. In an attempt to crystallize the protein; a number of variants were generated. One such construct; which includes the C-terminal region (residues 196-340); gave four different crystal forms which diffract in the 3. 5-6.0 A resolution range. | 10666640 | [
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] |
Preliminary X-ray crystallographic analysis of a plant defence protein, the polygalacturonase-inhibiting protein from Phaseolus vulgaris. | A leucine-rich repeat plant protein involved in resistance to pathogens; a polygalacturonase-inhibiting protein (PGIP-1) from Phaseolus vulgaris; has been crystallized and preliminary X-ray characterization has been performed. The protein contains ten repeats of a short (24 amino-acid) leucine-rich repeat motif. Single crystals of the protein were grown from vapour-diffusion experiments using PEG 2K monomethylether as precipitant; these crystals diffract to at least 2.3 A resolution. The space group is P2(1 | 10666641 | [
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Preliminary X-ray crystallographic analysis of a plant defence protein, the polygalacturonase-inhibiting protein from Phaseolus vulgaris. | ); with two molecules of PGIP-1 in the asymmetric unit; the crystals contain approximately 38% solvent. | 10666641 | [
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Crystallization of type I chloramphenicol acetyltransferase: an approach based on the concept of ionic strength reducers. | Chloramphenicol acetyltransferase (CAT) is responsible for bacterial resistance to chloramphenicol. It catalyzes inactivation of the antibiotic by acetyl-group transfer from acetyl CoA to one or both hydroxyl groups of chloramphenicol. Type I CAT possesses some unique properties which are not observed in other CAT variants. Type I CAT overexpressed in Escherichia coli was purified and crystals with a resolution limit of 2.22 A have been obtained using a novel procedure which is based on the concept of 'ioni | 10666642 | [
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Crystallization of type I chloramphenicol acetyltransferase: an approach based on the concept of ionic strength reducers. | c strength reducers'. The crystals have the symmetry of space group P1 and unit-cell parameters a = 96.46; b = 113.86; c = 114.21 A; alpha = 119.9; beta = 94.1; gamma = 98.6 degrees. These dimensions are consistent with four to six trimers per unit cell; corresponding to a solvent fraction ranging from 65 to 47%. | 10666642 | [
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Crystallization and preliminary crystallographic study of triple-helical DNA. | Single crystals of d(CTCCT(S)CCGCGCG).d(CGCGCGGAG) have been grown by the vapor-diffusion method using 2-methyl-2;4-pentanediol as a precipitant. The crystals are tetragonal; space group P4(2); with unit-cell parameters a = b = 53.8; c = 43.1 A; and diffract to 1.8 A resolution at a synchrotron X-ray beamline. In the crystal; the asymmetric unit contains one copy of the construct. The two halves of the structure are related by non-crystallographic twofold symmetry. These observations are consistent with the | 10666643 | [
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