[English] 日本語
![](img/lk-miru.gif)
- PDB-2rjh: Crystal structure of biosynthetic alaine racemase in D-cycloserin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2rjh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of biosynthetic alaine racemase in D-cycloserine-bound form from Escherichia coli | ||||||
![]() | 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 | ![]() | 294 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 86.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rjgC ![]() 3b8tC ![]() 3b8uC ![]() 3b8vC ![]() 3b8wC ![]() 1rcqS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41416.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-DCS / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
---|---|
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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 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: 78993 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RCQ Resolution: 2.4→15 Å / σ(F): 31 Details: This is a twinned structure, the detwin fraction is 0.400, and operator is 'h, -h-k, -l'.
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 37.124 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.374 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|