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Yorodumi- PDB-4q48: Structure of the RecQ Catalytic Core from Deinococcus radiodurans -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q48 | ||||||
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Title | Structure of the RecQ Catalytic Core from Deinococcus radiodurans | ||||||
Components | DNA helicase RecQ | ||||||
Keywords | DNA BINDING PROTEIN / DNA unwinding / helicase | ||||||
Function / homology | Function and homology information bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / chromosome / DNA recombination / DNA helicase / DNA replication ...bacterial nucleoid / four-way junction helicase activity / replisome / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / chromosome / DNA recombination / DNA helicase / DNA replication / nucleic acid binding / hydrolase activity / DNA repair / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.797 Å | ||||||
Authors | Chen, S.C. / Yang, C.S. / Chen, Y. | ||||||
Citation | Journal: Biomed Res Int / Year: 2014 Title: Crystal structure of Deinococcus radiodurans RecQ helicase catalytic core domain: the interdomain flexibility. Authors: Chen, S.C. / Huang, C.H. / Yang, C.S. / Way, T.D. / Chang, M.C. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q48.cif.gz | 202.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q48.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 4q48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q48 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q48 | HTTPS FTP |
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-Related structure data
Related structure data | 4q47C 1oywS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: Protein | Mass: 58409.527 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_1289 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RUU2 #2: Chemical | |
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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: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.1M HEPES (pH 7.7), 14% PEG 8K, 8% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.797→30 Å / Num. all: 32721 / Num. obs: 31511 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.543 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OYW Resolution: 2.797→27.312 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.797→27.312 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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