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Yorodumi- PDB-2rjg: Crystal structure of biosynthetic alaine racemase from Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rjg | ||||||
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Title | Crystal structure of biosynthetic alaine racemase from Escherichia coli | ||||||
Components | Alanine racemase | ||||||
Keywords | ISOMERASE / alpha/beta barrel / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / cell wall organization / pyridoxal phosphate binding / regulation of cell shape / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wu, D. / Hu, T. / Zhang, L. / Jiang, H. / Shen, X. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis Authors: Wu, D. / Hu, T. / Zhang, L. / Chen, J. / Du, J. / Ding, J. / Jiang, H. / Shen, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rjg.cif.gz | 290.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rjg.ent.gz | 234.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rjg_validation.pdf.gz | 512.4 KB | Display | wwPDB validaton report |
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Full document | 2rjg_full_validation.pdf.gz | 556.2 KB | Display | |
Data in XML | 2rjg_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 2rjg_validation.cif.gz | 84.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/2rjg ftp://data.pdbj.org/pub/pdb/validation_reports/rj/2rjg | HTTPS FTP |
-Related structure data
Related structure data | 2rjhC 3b8tC 3b8uC 3b8vC 3b8wC 1rcqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 41416.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: alr / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6B4, alanine racemase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PLP / #4: 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: 3.12 Å3/Da / Density % sol: 60.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M HEPES, 1.6M ammonium sulfate, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→164.399 Å / Num. obs: 78833 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.35 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RCQ Resolution: 2.4→15 Å / σ(F): 322 Details: This is a twinned structure, the detwin fraction is 0.400, and operator is 'h, -h-k, -l'.
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Solvent computation | Bsol: 39.431 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.118 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Xplor file |
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