+Open data
-Basic information
Entry | Database: PDB / ID: 5zwu | ||||||
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Title | Crystal structure of recombination mediator protein RecF | ||||||
Components | DNA replication and repair protein RecF | ||||||
Keywords | RECOMBINATION / recombination mediator protein | ||||||
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 | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Chaudhary, S.K. / Sekar, K. / Jeyakanthan, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of recombination mediator protein RecF Authors: Chaudhary, S.K. / Sekar, K. / Jeyakanthan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zwu.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zwu.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 5zwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zwu_validation.pdf.gz | 426.4 KB | Display | wwPDB validaton report |
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Full document | 5zwu_full_validation.pdf.gz | 432.7 KB | Display | |
Data in XML | 5zwu_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5zwu_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/5zwu ftp://data.pdbj.org/pub/pdb/validation_reports/zw/5zwu | HTTPS FTP |
-Related structure data
Related structure data | 2o5vS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37846.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: recF, TTHA0264 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5SLM9 |
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#2: 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: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 0.1M Sodium malonate pH 7.0, 0.1M HEPES pH 7.0, 0.5 % v/v Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→51.13 Å / Num. obs: 60237 / % possible obs: 99.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.58→1.6 Å / Rmerge(I) obs: 0.355 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O5V Resolution: 1.58→51.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.089 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.334 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→51.13 Å
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Refine LS restraints |
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