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Yorodumi- PDB-1zuw: Crystal structure of B.subtilis glutamate racemase (RacE) with D-Glu -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zuw | ||||||
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Title | Crystal structure of B.subtilis glutamate racemase (RacE) with D-Glu | ||||||
Components | glutamate racemase 1 | ||||||
Keywords | ISOMERASE / glutamate racemase / (R)-glutamate / Peptidoglycan biosynthesis | ||||||
Function / homology | Function and homology information amino-acid racemase activity / glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Ruzheinikov, S.N. / Taal, M.A. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Substrate-Induced Conformational Changes in Bacillus subtilis Glutamate Racemase and Their Implications for Drug Discovery Authors: Ruzheinikov, S.N. / Taal, M.A. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Expression, purification and preliminary X-ray analysis of crystals of Bacillus subtilis glutamate racemase Authors: Taal, M.A. / Sedelnikova, S.E. / Ruzheinikov, S.N. / Baker, P.J. / Rice, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zuw.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zuw.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 1zuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zuw ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zuw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer generated by chains A and C in the asymmetric unit by the operations: -y, x-y-1, z-1 and -x+y, -x-1, z-l. |
-Components
#1: Protein | Mass: 30029.326 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: racE / Production host: Escherichia coli (E. coli) / References: UniProt: P94556, glutamate racemase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG 3350, 0.2 M di-Ammonium tartrate , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.75→10 Å / Num. obs: 82597 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.79 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Refine LS restraints |
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