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Yorodumi- PDB-5z69: Structure of the recombination mediator protein RecF-ATPrS in Rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z69 | ||||||
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Title | Structure of the recombination mediator protein RecF-ATPrS in RecFOR pathway | ||||||
Components | DNA replication and repair protein RecF | ||||||
Keywords | DNA BINDING PROTEIN / recF / DNA repair / recombination mediator / RecFOR / Rad50 | ||||||
Function / homology | Function and homology information SOS response / single-stranded DNA binding / DNA replication / DNA repair / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.102 Å | ||||||
Authors | Tang, Q. / Liu, Y.-P. / Yan, X.-X. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair. Authors: Tang, Q. / Liu, Y.P. / Shan, H.H. / Tian, L.F. / Zhang, J.Z. / Yan, X.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z69.cif.gz | 327.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z69.ent.gz | 274.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z69_validation.pdf.gz | 746.7 KB | Display | wwPDB validaton report |
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Full document | 5z69_full_validation.pdf.gz | 762.8 KB | Display | |
Data in XML | 5z69_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 5z69_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z69 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z69 | 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: 43194.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria) Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: recF, TTE0004 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8RDL3 #2: Chemical | ChemComp-AGS / | #3: 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: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 300 mM NaCl, 100 mM Tris-Hcl, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.005 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 913873 / % possible obs: 99.6 % / Redundancy: 7.6 % / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Resolution: 2.102→19.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→19.835 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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