[English] 日本語
![](img/lk-miru.gif)
- PDB-3b8v: Crystal structure of Escherichia coli alaine racemase mutant E221K -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3b8v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Escherichia coli alaine racemase mutant E221K | ||||||
![]() | Alanine racemase | ||||||
![]() | ISOMERASE / alpha/beta barrel / Cell shape / Cell wall biogenesis/degradation / Peptidoglycan synthesis / Pyridoxal phosphate | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wu, D. / Hu, T. / Zhang, L. / Jiang, H. / Shen, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 291.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 234.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 519.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 564.3 KB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 84.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rjgSC ![]() 2rjhC ![]() 3b8tC ![]() 3b8uC ![]() 3b8wC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41416.301 Da / Num. of mol.: 4 / Mutation: E221K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.72 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.1M MES, 1.6M ammonium sulfate, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 18, 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: 2.6→164.399 Å / Num. obs: 62549 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 5.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RJG Resolution: 2.6→15 Å / σ(F): 6 Details: This is a twinned structure, the detwin fraction is 0.400, and operator is 'h, -h-k, -l'.
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 41.543 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.421 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|