+Open data
-Basic information
Entry | Database: PDB / ID: 2c2u | ||||||
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Title | Dps from Deinococcus radiodurans | ||||||
Components | DNA-BINDING STRESS RESPONSE PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / DPS / IRON / DEINOCOCCUS RADIODURANS / DNA-BINDING | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Romao, C.V. / Mitchell, E. / McSweeney, S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2006 Title: The Crystal Structure of Deinococcus Radiodurans Dps Protein (Dr2263) Reveals the Presence of a Novel Metal Centre in the N Terminus. Authors: Romao, C.V. / Mitchell, E. / Mcsweeney, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c2u.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c2u.ent.gz | 77.9 KB | Display | PDB format |
PDBx/mmJSON format | 2c2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c2u ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2u | HTTPS FTP |
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-Related structure data
Related structure data | 2c2fSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23050.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RS64 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-FE / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 8.5 Details: 200MM LITHIUM SULFATE 100MM TRIS-HCL PH8.5 15% PEG4000, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 24, 2005 / Details: MULTI-LAYER MIRROR |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→21.31 Å / Num. obs: 99021 / % possible obs: 99.6 % / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C2F Resolution: 1.1→21.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.663 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 29 AMINO ACID RESIDUES WERE NOT MODELLED DUE TO THE FACT THAT WAS NOT POSSIBLE TO ALLOCATE THE ELECTRON DENSITY.
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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: 8.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→21.3 Å
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Refine LS restraints |
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