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Yorodumi- PDB-2v1c: Crystal structure and mutational study of RecOR provide insight i... -
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-Basic information
Entry | Database: PDB / ID: 2v1c | ||||||
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Title | Crystal structure and mutational study of RecOR provide insight into its role in DNA repair | ||||||
Components |
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Keywords | RECOMBINATION / HOMOLOGOUS RECOMBINATION / RECFOR PATHWAY / DNA RECOMBINATION / DNA BINDING / ZINC-FINGER / METAL-BINDING / RECOR COMPLEX / HYPOTHETICAL PROTEIN / DEINOCOCCUS RADIODURANS / RECR / ZINC / RECO / DNA DAMAGE / DNA REPAIR | ||||||
Function / homology | Function and homology information bacterial nucleoid / double-strand break repair / DNA recombination / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Timmins, J. / Leiros, I. / McSweeney, S. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Crystal Structure and Mutational Study of Recor Provide Insight Into its Mode of DNA Binding. Authors: Timmins, J. / Leiros, I. / Mcsweeney, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1c.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1c.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v1c_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 2v1c_full_validation.pdf.gz | 506.8 KB | Display | |
Data in XML | 2v1c_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 2v1c_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1c ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23752.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZNA2 #2: Protein | | Mass: 26376.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RW50 #3: Chemical | |
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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: 2.6 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Details: 0.1 M MES PH 6.5, 10% DIOXANE, 1.6 M AMMONIUM SULPHATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 26, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→45 Å / Num. obs: 7194 / % possible obs: 95.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 96 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.8→4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1VDD,1W3S Resolution: 3.8→71.25 Å / Cor.coef. Fo:Fc: 0.644 / Cor.coef. Fo:Fc free: 0.667 / SU ML: 3.138 / Cross valid method: THROUGHOUT / ESU R: 1.508 / ESU R Free: 1.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL REPRESENTS A RIGID-BODY REFINEMENT WHERE EACH PROTEIN MONOMER WAS TREATED AS ONE RIGID BODY, FOLLOWED BY A SINGLE ROUND OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS MODEL REPRESENTS A RIGID-BODY REFINEMENT WHERE EACH PROTEIN MONOMER WAS TREATED AS ONE RIGID BODY, FOLLOWED BY A SINGLE ROUND OF MANUAL REMODELLING WITH APPROXIMATIVE FITTING OF SIDECHAINS. THE LIMITED NUMBER OF OBSERVATIONS PRECLUDED POSITIONAL REFINEMENT OF INDIVIDUAL ATOMS. RESIDUES A1, A200-A220, B1, B200-B220, C1-C2, C237-C244 ARE DISORDERED.
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Displacement parameters | Biso mean: 96 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→71.25 Å
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LS refinement shell | Resolution: 3.8→3.9 Å / Total num. of bins used: 20 /
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