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Open data
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Basic information
Entry | Database: PDB / ID: 2xjo | ||||||
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Title | Crystal structure of Streptococcus suis Dpr with nickel | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 747.5 KB | Display | ![]() |
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PDB format | ![]() | 628.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.8 KB | Display | ![]() |
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Full document | ![]() | 501.8 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 59.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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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 |
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-Non-polymers , 5 types, 778 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-EPE / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.4 % / Description: NONE |
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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 |
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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: 1.48746 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 118580 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 11.029 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.177 / 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.
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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: 14.685 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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