+
Open data
-
Basic information
Entry | Database: PDB / ID: 2xjm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Streptococcus suis Dpr with cobalt | ||||||
![]() | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
![]() | OXIDOREDUCTASE / IRON STORAGE / METAL-BINDING | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Haikarainen, T. / Thanassoulas, A. / Stavros, P. / Nounesis, G. / Haataja, S. / Papageorgiou, A.C. | ||||||
![]() | ![]() Title: Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr. Authors: Haikarainen, T. / Thanassoulas, A. / Stavros, P. / Nounesis, G. / Haataja, S. / Papageorgiou, A.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 732.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 615 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 534.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 557.7 KB | Display | |
Data in XML | ![]() | 72.6 KB | Display | |
Data in CIF | ![]() | 101.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 18641.014 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0CB53, Oxidoreductases; Oxidizing metal ions |
---|
-Non-polymers , 5 types, 829 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-EPE / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 44 % Description: FRIEDEL_LAW=FALSE WAS USED DURING DATA PROCESSING, AND A TOTAL OF 169544 REFLECTIONS WERE COLLECTED. |
---|---|
Crystal grow | pH: 7.4 Details: 30 - 35 % (V/V) PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH (PH 7.4) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MARMOSAIC / Detector: CCD / Date: Oct 10, 2008 / Details: VERTICALLY FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.60846 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 88486 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.4 / % possible all: 76.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.3→24.91 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.448 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.295 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→24.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|