+Open data
-Basic information
Entry | Database: PDB / ID: 2f7n | ||||||
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Title | Structure of D. radiodurans Dps-1 | ||||||
Components | DNA-binding stress response protein, Dps family | ||||||
Keywords | DNA BINDING PROTEIN / 4-helix bundle | ||||||
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 / SAD / Resolution: 2 Å | ||||||
Authors | Lee, Y.H. / Kim, S.G. / Bhattacharyya, G. / Grove, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structure of Dps-1, a functionally distinct Dps protein from Deinococcus radiodurans. Authors: Kim, S.G. / Bhattacharyya, G. / Grove, A. / Lee, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f7n.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f7n.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f7n_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 2f7n_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 2f7n_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2f7n_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/2f7n ftp://data.pdbj.org/pub/pdb/validation_reports/f7/2f7n | HTTPS FTP |
-Related structure data
Similar structure data |
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-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) Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 15807254, UniProt: Q9RS64*PLUS | ||||
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#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-SO4 / | #4: 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: 2.65 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM MES; 100mM cobalt chloride; 2M anmmonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 2005 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 31997 / Num. obs: 16568 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 9.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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