+Open data
-Basic information
Entry | Database: PDB / ID: 5x4h | ||||||
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Title | The crystal structure of Pyrococcus furiosus RecJ (wild-type) | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / Archaeal RecJ / CMG interaction domain / Nuclease activity / GINS / interaction | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å | ||||||
Authors | Li, M.J. / Yi, G.S. / Yu, F. / Zhou, H. / Chen, J.N. / Xu, C.Y. / Wang, F.P. / Xiao, X. / He, J.H. / Liu, X.P. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Authors: Li, M.J. / Yi, G.S. / Yu, F. / Zhou, H. / Chen, J.N. / Xu, C.Y. / Wang, F.P. / Xiao, X. / He, J.H. / Liu, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x4h.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x4h.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 5x4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/5x4h ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x4h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56423.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF2055 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZE0 |
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#2: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.74 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 4.3% w/v PEG 2000 MME, 50 mM Bicine pH 8.8, 28.6% w/v PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 10538 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 10.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.801→49.033 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.76 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→49.033 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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