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Yorodumi- PDB-4ad8: Crystal structure of a deletion mutant of Deinococcus radiodurans RecN -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ad8 | ||||||
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Title | Crystal structure of a deletion mutant of Deinococcus radiodurans RecN | ||||||
Components | DNA REPAIR PROTEIN RECN | ||||||
Keywords | DNA BINDING PROTEIN / DNA REPAIR / ATPASE DOMAIN | ||||||
Function / homology | Function and homology information SOS response / response to radiation / DNA recombination / DNA repair / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.998 Å | ||||||
Authors | Pellegrino, S. / Radzimanowski, J. / de Sanctis, D. / McSweeney, S. / Timmins, J. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Structural and Functional Characterization of an Smc-Like Protein Recn: New Insights Into Double-Strand Break Repair. Authors: Pellegrino, S. / Radzimanowski, J. / De Sanctis, D. / Erba, E.B. / Mcsweeney, S. / Timmins, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ad8.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ad8.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ad8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4ad8 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4ad8 | HTTPS FTP |
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-Related structure data
Related structure data | 4abxC 4abySC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 55154.637 Da / Num. of mol.: 1 Fragment: HEAD AND PARTIAL COILED-COIL DOMAINS, RESIDUES 1-237,305-564 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 / Variant (production host): STAR / References: UniProt: Q9WXF2, EC: 3.6.1.3 |
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Sequence details | LINKER PEPTIDE ESSKHPTSLV |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.6 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 10% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 4→47 Å / Num. obs: 5430 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 87.28 Å2 / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 4→4.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ABY Resolution: 3.998→47.031 Å / SU ML: 1.39 / σ(F): 1.38 / Phase error: 38.56 / Stereochemistry target values: ML Details: THE B-FACTOR VALUES HAVE BEEN SET TO THE ESTIMATE FROM THE WILSON PLOT DETERMINED BY XDS AND NOT FURTHER REFINED. THIS IS OWING TO THE LOW RESOLUTION OF THE DATA.
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.671 Å2 / ksol: 0.285 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 70 Å2
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Refinement step | Cycle: LAST / Resolution: 3.998→47.031 Å
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Refine LS restraints |
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LS refinement shell |
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