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Yorodumi- PDB-3cmw: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cmw | ||||||
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Title | Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures | ||||||
Components |
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Keywords | recombination/DNA / homologous recombination / recombination-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pavletich, N.P. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Authors: Chen, Z. / Yang, H. / Pavletich, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cmw.cif.gz | 631.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cmw.ent.gz | 499 KB | Display | PDB format |
PDBx/mmJSON format | 3cmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cmw_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 3cmw_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 3cmw_validation.xml.gz | 64.6 KB | Display | |
Data in CIF | 3cmw_validation.cif.gz | 96.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cmw ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cmw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4517.935 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 182240.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7G6 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ALF / #5: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: RecA5 fusion protein was incubated with a 3-fold molar excess of ssDNA in the original protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0. Crystals of the RecA5- ...Details: RecA5 fusion protein was incubated with a 3-fold molar excess of ssDNA in the original protein buffer supplemented with 2 mM ADP, 10 mM MgCl2 and 8 mM AlF4, pH 6.0. Crystals of the RecA5-(ADP-AlF4-Mg)5-(dT)15 complex were grown from 50 mM Tris-Cl, 9% (w/v) PVP K15, 32% (v/v) MPD, 10 mM DTT, pH 8.0. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
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Detector | Date: Feb 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 81934 |
-Processing
Software | Name: REFMAC / Version: 5.3.0036 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 31.216 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Total num. of bins used: 20
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