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Yorodumi- PDB-3dfg: Crystal Structure of RecX: A Potent Inhibitor Protein of RecA fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dfg | ||||||
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Title | Crystal Structure of RecX: A Potent Inhibitor Protein of RecA from Xanthomonas campestris | ||||||
Components | Regulatory protein recX | ||||||
Keywords | RECOMBINATION / RecX crystal structure / RecA / homologous recombination / Xanthomonas campestris / tandem repeats / three-helix bundle / Cytoplasm | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Yang, C.Y. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of RecX: a potent regulatory protein of RecA from Xanthomonas campestris. Authors: Yang, C.Y. / Chin, K.H. / Yang, M.T. / Wang, A.H.J. / Chou, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dfg.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dfg.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dfg_validation.pdf.gz | 417.8 KB | Display | wwPDB validaton report |
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Full document | 3dfg_full_validation.pdf.gz | 418.7 KB | Display | |
Data in XML | 3dfg_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 3dfg_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/3dfg ftp://data.pdbj.org/pub/pdb/validation_reports/df/3dfg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18015.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Gene: XCC17 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P9X1 |
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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: 2.64 Å3/Da / Density % sol: 53.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97997, 0.96472 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→30 Å / Num. obs: 55383 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 4 | |||||||||
Reflection shell | Resolution: 1.5→1.55 Å |
-Processing
Software |
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Refinement | Resolution: 1.5→26.35 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 127458 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.44 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.06 Å2 / Biso mean: 26.099 Å2 / Biso min: 10.92 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→26.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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