Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus

1998 ◽  
Vol 54 (1) ◽  
pp. 127-128 ◽  
Author(s):  
Takanori Kumagai ◽  
Kengo Muta ◽  
Yasuyuki Matoba ◽  
Yoshiaki Kawano ◽  
Nobuo Kamiya ◽  
...  
Keyword(s):  
Binding Protein ◽  
Diffusion Method ◽  
X Rays ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Diffraction Intensity ◽  
Data Set ◽  
X Ray ◽  
Peg 4000 ◽  
Cell Dimensions

A bleomycin-binding protein (BLMA) produced by bleomycin-producing Streptomyces verticullus was crystallized in a form suitable for X-ray diffraction analysis using the vapor-diffusion method. Crystals were grown at pH 5.7, in 0.2 M NH4 actate and 0.1 M Na acetate, using 30% PEG 4000 as a precipitant. They belong to the orthorhombic system, with space group P21212, cell dimensions a = 54.90, b = 67.94, c = 35.60 Å, and one BLMA molecule in the asymmetric unit. The crystals diffract X-rays well and the diffraction intensity data was collected up to 1.5 Å resolution with a merging R value of 0.054 at beamline 6B of the Photon Factory. The diffraction data set is 94% complete.

Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus

1999 ◽  
Vol 55 (7) ◽  
pp. 1353-1355 ◽  
Author(s):  
C. Charron ◽  
F. Talfournier ◽  
M. N. Isupov ◽  
G. Branlant ◽  
J. A. Littlechild ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Data Set ◽  
Hyperthermophilic Archaeon ◽  
X Ray ◽  
Cell Dimensions ◽  
Methanothermus Fervidus ◽  
Unit Cell Dimensions

The homotetrameric holo-D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus has been crystallized in the presence of NADP+ using the hanging-drop vapour-diffusion method. Crystals grew from a solution containing 2-methyl-2,4-pentanediol and magnesium acetate. A native data set has been collected to 2.1 Å using synchrotron radiation and cryocooling. Diffraction data have been processed in the orthorhombic system (space group P21212) with unit-cell dimensions a = 136.7, b = 153.3, c = 74.9 Å and one tetramer per asymmetric unit.

scholarly journals Crystallization and preliminary X-ray diffraction analysis ofBacillus subtilisYwfE, anL-amino-acid ligase

2012 ◽  
Vol 68 (2) ◽  
pp. 203-206 ◽  
Author(s):  
Takeo Tsuda ◽  
Tomomi Suzuki ◽  
Shuichi Kojima
Keyword(s):  
Amino Acid ◽  
Diffusion Method ◽  
Dependent Manner ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters

Bacillus subtilisYwfE, an L-amino-acid ligase, catalyzes the formation of an α-dipeptide from L-amino acids in an ATP-dependent manner. In order to elucidate the substrate-recognition mode and the reaction mechanism of this ligase, native and selenomethionine-derivatized (SeMet) crystals of YwfE in the presence of ADP, MgCl2and the dipeptide L-Ala-L-Gln were obtained using the hanging-drop vapour-diffusion method. These crystals diffracted to 1.9 and 2.8 Å resolution, respectively. Preliminary SAD phase calculations using the data set from the SeMet crystal suggested that the crystal belonged to the hexagonal space groupP6522, with unit-cell parametersa=b= 90.85,c = 250.31 Å, and contained one molecule in the asymmetric unit with a solvent content of 57.3%.

Crystallization and preliminary X-ray studies of hORF6, a novel human antioxidant enzyme

1998 ◽  
Vol 54 (3) ◽  
pp. 436-436 ◽  
Author(s):  
Hee-Jeong Choi ◽  
Sang Won Kang ◽  
Chul-Hak Yang ◽  
Sue Goo Rhee ◽  
Seong-Eon Ryu
Keyword(s):  
Antioxidant Enzyme ◽  
Unit Cell ◽  
X Rays ◽  
Asymmetric Unit ◽  
Data Set ◽  
X Ray ◽  
Space Groups ◽  
Cell Dimensions ◽  
Hanging Drop Method ◽  
Unit Cell Dimensions

HORF6 is a member of the novel antioxidant enzyme family found in humans. A recombinant form of hORF6 expressed and purified from E. coli has been crystallized by the hanging-drop method using various PEG's as precipitating agents. HORF6 crystallizes in two different monoclinic space groups, P21 and C2. The P21 crystals have unit-cell dimensions of a = 47.85, b = 75.17, c = 63.30 Å and β = 110.21° and contain two monomers per asymmetric unit, while the C2 crystals have unit-cell dimensions of a = 165.27, b = 95.44, c = 166.44 Å and β = 128.97° and contain more than six monomers per asymmetric unit. The P21 crystals with the smaller unit cell diffract X-rays better and behave well for the X-ray analysis. A native data set from a single crystal of the P21 space group gas been collected to 2.0 Å resolution.

Crystallization and preliminary X-ray diffraction studies of α-toxin from two different strains (NCTC8237 and CER89L43) of Clostridium perfringens

1998 ◽  
Vol 54 (6) ◽  
pp. 1425-1428 ◽  
Author(s):  
A. K. Basak ◽  
A. Howells ◽  
J. T. Eaton ◽  
D. S. Moss ◽  
C. E. Naylor ◽  
...  
Keyword(s):  
Clostridium Perfringens ◽  
Diffusion Method ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Gene Encoding ◽  
Space Group ◽  
X Ray ◽  
E Coli ◽  
Cell Dimensions ◽  
Different Strains

The α-toxin of Clostridium perfringens is the major virulence determinant for gas gangrene in man. The gene encoding the α-toxin has been cloned into E. coli from two strains of the bacterium (NCTC8237 and CER89L43) and subsequently purified to homogeneity. The two strains of α-toxin differ by five amino acids, resulting in the toxin from NCTC8237 being sensitive to chymotrypsin digestion while that from CER89L43 is resistant. The α-toxin from each of these strains has been crystallized in two different forms by the hanging-drop vapour-diffusion method at 293 K. CER89L43 form I crystals belong to space group R32 and have two molecules in the crystallographic asymmetric unit and a unit cell with a = b = 151.4, c = 195.5 Å, α = β = 90, γ = 120°. The crystals diffracted to d min = 1.90 Å. The characteristics of the NCTC8237 form I crystals have already been reported. The form II crystals from both strains belong to space group C2221 with one molecule in the crystallographic asymmetric unit and, for strain CER89L43, have cell dimensions a = 61.05, b = 177.50, c = 79.05 Å, α = β = γ = 90°, while for strain NCTC8237 the cell dimensions are a = 60.50, b = 175.70, c = 80.20 Å, α = β = γ = 90°. The crystals diffracted to maximum resolutions of 1.85 and 2.1 Å for the CER89L43 and the NCTC8237 strains, respectively.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

2012 ◽  
Vol 68 (7) ◽  
pp. 802-805 ◽  
Author(s):  
Lei Han ◽  
Zheng Liu ◽  
Xinqi Liu ◽  
Dewen Qiu
Keyword(s):  
Pathogenic Fungus ◽  
Sodium Formate ◽  
Diffusion Method ◽  
Effector Protein ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Dispersion Method ◽  
Data Set ◽  
X Ray ◽  
Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

scholarly journals Crystallization and X-ray diffraction analysis of native and selenomethionine-substituted PhyH-DI fromBacillussp. HJB17

2017 ◽  
Vol 73 (11) ◽  
pp. 607-611
Author(s):  
Fang Lu ◽  
Bei Zhang ◽  
Yong Liu ◽  
Ying Song ◽  
Gangxing Guo ◽  
...  
Keyword(s):  
Unit Cell ◽  
Diffusion Method ◽  
Data Sets ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Solvent Content ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Phytases are phosphatases that hydrolyze phytates to less phosphorylatedmyo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase fromBacillussp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate. Crystals of native and selenomethionine-substituted PhyH-DI were obtained using the vapour-diffusion method in a condition consisting of 0.2 Msodium chloride, 0.1 MTris pH 8.5, 25%(w/v) PEG 3350 at 289 K. X-ray diffraction data were collected to 3.00 and 2.70 Å resolution, respectively, at 100 K. Native PhyH-DI crystals belonged to space groupC121, with unit-cell parametersa = 156.84,b = 45.54,c = 97.64 Å, α = 90.00, β = 125.86, γ = 90.00°. The asymmetric unit contained two molecules of PhyH-DI, with a corresponding Matthews coefficient of 2.17 Å3 Da−1and a solvent content of 43.26%. Crystals of selenomethionine-substituted PhyH-DI belonged to space groupC2221, with unit-cell parametersa = 94.71,b= 97.03,c= 69.16 Å, α = β = γ = 90.00°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.44 Å3 Da−1and a solvent content of 49.64%. Initial phases for PhyH-DI were obtained from SeMet SAD data sets. These data will be useful for further studies of the structure–function relationship of PhyH-DI.

scholarly journals Expression, purification, crystallization and preliminary X-ray analysis of tannase fromLactobacillus plantarum

2013 ◽  
Vol 69 (4) ◽  
pp. 456-459 ◽  
Author(s):  
Mingbo Wu ◽  
Xiaohong Peng ◽  
Hua Wen ◽  
Qin Wang ◽  
Qianming Chen ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Gallic Acid ◽  
Diffusion Method ◽  
Ester Bond ◽  
Asymmetric Unit ◽  
Data Set ◽  
X Ray ◽  
Vapour Diffusion ◽  
Serine Esterases ◽  
Hydrolysis Of

Tannase catalyses the hydrolysis of the galloyl ester bond of tannins to release gallic acid. It belongs to the serine esterases and has wide applications in the food, feed, beverage, pharmaceutical and chemical industries. The tannase fromLactobacillus plantarumwas cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method with microseeding. The crystals belonged to space groupP1, with unit-cell paramtersa= 46.5,b= 62.8,c= 83.8 Å, α = 70.4, β = 86.0, γ = 79.4°. Although the enzyme exists mainly as a monomer in solution, it forms a dimer in the asymmetric unit of the crystal. The crystals diffracted to beyond 1.60 Å resolution using synchrotron radiation and a complete data set was collected to 1.65 Å resolution.

scholarly journals Cloning, expression, purification, crystallization and preliminary crystallographic analysis of 5-aminolaevulinic acid dehydratase fromBacillus subtilis

2010 ◽  
Vol 66 (9) ◽  
pp. 1053-1055 ◽  
Author(s):  
Qianda Lu ◽  
Jinming Ma ◽  
Hui Rong ◽  
Jun Fan ◽  
Ye Yuan ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Gene Encoding ◽  
Data Set ◽  
X Ray ◽  
Aminolaevulinic Acid ◽  
Acid Dehydratase ◽  
Strain Bl21 ◽  
Aminolaevulinic Acid Dehydratase

5-Aminolaevulinic acid dehydratase (ALAD), a crucial enzyme in the biosynthesis of tetrapyrrole, catalyses the condensation of two 5-aminolaevulinic acid (ALA) molecules to form porphobilinogen (PBG). The gene encoding ALAD was amplified from genomic DNA ofBacillus subtilisand the protein was overexpressed inEscherichia colistrain BL21 (DE3). The protein was purified and crystallized with an additional MGSSHHHHHHSSGLVPRGSH– tag at the N-terminus of the target protein. Diffraction-quality single crystals were obtained by the hanging-drop vapour-diffusion method. An X-ray diffraction data set was collected at a resolution of 2.7 Å.

Structural studies of technetium complexes. V. The preparation and crystal structure of Dichlorobis(diethyldithiocarbamato)thionitrosyltechnetium(III)

1984 ◽  
Vol 37 (4) ◽  
pp. 751 ◽  
Author(s):  
J Baldas ◽  
J Bonnyman ◽  
MF Mackay ◽  
GA Williams
Keyword(s):  
Crystal Structure ◽  
Positive Charge ◽  
Mirror Plane ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
Coordination Environment ◽  
X Ray

Dichlorobis(diethyldithiocarbamato)thionitrosyltechnetium(III), [Tc(S2CNEt2)2Cl2(NS)], has been prepared by the reaction of [Tc(S2CNEt2)2N] with either disulfur dichloride or thionyl chloride. The crystal structure of [TC(S2CNEt2)2Cl2(NS)] has been determined by single-crystal X-ray diffraction methods at 15�C. Crystals are orthorhombic, space group Pcmn, with a 8.936(1), b 15.681(1), c 28.445(7) �, and Z 8. Automatic diffractometry has provided significant Bragg intensities for 2078 independent reflections, and the structure has been refined by full-matrix least-squares methods to R 0.078. The crystal lattice is disordered across a non-crystallographic mirror plane, the degree of disorder being 4.0(2)% for the crystal described above, and 21.9(7)% for another crystal initially used to obtain an intensity data set. There are two independent molecules of [Tc(S2CNEt2)2Cl2(NS)] in the asymmetric unit, and in each the technetium atom is seven-coordinate with a pentagonal-bipyramidal coordination environment. The Tc=N=S bonding is linear with Tc=N c. 1.75 and N=S c. 1.52 �, which indicates that the thionitrosyl group is a three-electron donor with a formal positive charge. This is only the third crystal structure of a complex containing the thionitrosyl group to be determined, and the first for technetium.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of AntE, a crotonyl-CoA carboxylase/reductase fromStreptomycessp. NRRL 2288

2014 ◽  
Vol 70 (6) ◽  
pp. 734-737 ◽  
Author(s):  
Lihan Zhang ◽  
Jing Chen ◽  
Takahiro Mori ◽  
Yan Yan ◽  
Wen Liu ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Antimycin A ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Unsaturated Acyl ◽  
Reductive Carboxylation

AntE fromStreptomycessp. NRRL 2288 is a crotonyl-CoA carboxylase/reductase that catalyzes the reductive carboxylation of various α,β-unsaturated acyl-CoAs to provide the building block at the C7 position for antimycin A biosynthesis. Recombinant AntE expressed inEscherichia coliwas crystallized by the sitting-drop vapour-diffusion method. The crystals belonged to space groupI222 orI212121, with unit-cell parametersa= 76.4,b= 96.7,c= 129.6 Å, α = β = γ = 90.0°. A diffraction data set was collected at the KEK Photon Factory to 2.29 Å resolution.

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