[English] 日本語
![](img/lk-miru.gif)
- PDB-4jcu: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomeras... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jcu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1 | ||||||
![]() | 5-carboxymethyl-2-hydroxymuconate isomerase | ||||||
![]() | ISOMERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / Triangular trimer assembly / PROTEIN STRUCTURE INITIATIVE / 5-carboxymethyl-2-hydroxymuconate | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: Crystal structure of a 5-carboxymethyl-2-hydroxymuconate isomerase from Deinococcus radiodurans R1 Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 71.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17071.732 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Gene: DR_A0227 / Plasmid: PET3A / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.85 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2M Ammonium acetate, 0.1M Sodium acetate, 25% PEG 4000, 5% Trimethylamine N-oxide dihydrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2013 / Details: Mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 21677 / Num. obs: 21677 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 1749 / % possible all: 99 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.276 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.46 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.398→2.46 Å / Total num. of bins used: 20
|