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Yorodumi- PDB-5z68: Structure of the recombination mediator protein RecF-ATP in RecFO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z68 | ||||||
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Title | Structure of the recombination mediator protein RecF-ATP 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 DNA synthesis involved in DNA repair / SOS response / double-strand break repair / single-stranded DNA binding / DNA replication / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 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 | 5z68.cif.gz | 306 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z68.ent.gz | 253.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z68 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z68 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43389.980 Da / Num. of mol.: 4 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-ATP / #3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-MG / #5: 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: 3.92 Å3/Da / Density % sol: 68.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8M ammonium sulfate, 100 mM Tris-Hcl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.005 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 3→3.05 Å |
-Processing
Software |
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Refinement | Resolution: 3→19.863 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→19.863 Å
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Refine LS restraints |
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LS refinement shell |
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