[English] 日本語
Yorodumi- PDB-3b8u: Crystal structure of Escherichia coli alaine racemase mutant E221A -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b8u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Escherichia coli alaine racemase mutant E221A | ||||||
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: 3 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3b8u.cif.gz | 285.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3b8u.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 3b8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b8u_validation.pdf.gz | 510.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3b8u_full_validation.pdf.gz | 569.6 KB | Display | |
Data in XML | 3b8u_validation.xml.gz | 62.2 KB | Display | |
Data in CIF | 3b8u_validation.cif.gz | 83.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/3b8u ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b8u | HTTPS FTP |
-Related structure data
Related structure data | 2rjgSC 2rjhC 3b8tC 3b8vC 3b8wC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41358.199 Da / Num. of mol.: 4 / Mutation: E221A 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(DE3) / References: UniProt: P0A6B4, alanine racemase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 16, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→164.399 Å / Num. obs: 39617 / % possible obs: 97.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.164 / Rsym value: 0.164 / Net I/σ(I): 4.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RJG Resolution: 3→15 Å / σ(F): 38 Details: This is a twinned structure, the detwin fraction is 0.400, and operator is 'h, -h-k, -l'.
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 32.071 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.606 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→15 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|