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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 | ||||||
Components | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / IRON STORAGE / METAL-BINDING | ||||||
| Function / homology | Function and homology informationOxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
| Biological species | STREPTOCOCCUS SUIS (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å | ||||||
Authors | Haikarainen, T. / Thanassoulas, A. / Stavros, P. / Nounesis, G. / Haataja, S. / Papageorgiou, A.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2xjo.cif.gz | 747.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2xjo.ent.gz | 628.3 KB | Display | PDB format |
| PDBx/mmJSON format | 2xjo.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xjo ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xjo | HTTPS FTP |
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-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.) STREPTOCOCCUS SUIS (bacteria) / Production host: ![]() References: UniProt: P0CB53, Oxidoreductases; Oxidizing metal ions |
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-Non-polymers , 5 types, 778 molecules 








| #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.48746 |
| 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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STREPTOCOCCUS SUIS (bacteria)
X-RAY DIFFRACTION
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