[English] 日本語
![](img/lk-miru.gif)
- PDB-5krv: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulni... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5krv | ||||||
---|---|---|---|---|---|---|---|
Title | 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine | ||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Function / homology | ![]() isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / NADPH binding / manganese ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ussin, N. / Abdulsalam, R.W. / Magee, P. / Chruszcz, M. | ||||||
![]() | ![]() Title: Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. Authors: Ussin, N.K. / Bagnell, A.M. / Offermann, L.R. / Abdulsalam, R. / Perdue, M.L. / Magee, P. / Chruszcz, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 314.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 257.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 486 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kqoSC ![]() 5krrC ![]() 5kryC ![]() 5ks1C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46149.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CMCP6 / Gene: dxr, VV1_1866 / Plasmid: pJExpress411 / Production host: ![]() ![]() References: UniProt: Q8DBF5, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
---|
-Non-polymers , 5 types, 189 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SRT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SRT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ARG / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SRT / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.8 M Sodium potassium tartrate 20% (w/v) PEG 3350 5 mM Arginine |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 53084 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.871 / % possible all: 98.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5KQO Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.277 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|