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Yorodumi- PDB-6hm3: Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hm3 | ||||||
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Title | Crystal structure of Rad4 BRCT1,2 in complex with a Sld3 phosphopeptide | ||||||
Components |
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Keywords | CELL CYCLE / BRCT domain phosphopeptide recognition | ||||||
Function / homology | Function and homology information mitotic spindle pole body / mitotic DNA damage checkpoint signaling / chromatin => GO:0000785 / DNA replication preinitiation complex / mitotic DNA replication initiation / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity ...mitotic spindle pole body / mitotic DNA damage checkpoint signaling / chromatin => GO:0000785 / DNA replication preinitiation complex / mitotic DNA replication initiation / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / meiotic cell cycle / mitotic spindle / site of double-strand break / chromatin / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77263620528 Å | ||||||
Authors | Day, M. / Rappas, M. / Oliver, A.W. / Pearl, L.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2018 Title: BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands. Authors: Day, M. / Rappas, M. / Ptasinska, K. / Boos, D. / Oliver, A.W. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hm3.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hm3.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hm3 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hm3 | HTTPS FTP |
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-Related structure data
Related structure data | 6hm4C 6hm5C 4bmcS 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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Unit cell |
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-Components
#1: Protein | Mass: 21236.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: rad4, cut5, SPAC23C4.18c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32372 | ||||
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#2: Protein/peptide | Mass: 3411.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09761 | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: Unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→42.2041207773 Å / Num. obs: 27589 / % possible obs: 98.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 26.18 Å2 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.77→1.82 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BMC Resolution: 1.77263620528→42.2041207773 Å / SU ML: 0.198039347248 / Cross valid method: FREE R-VALUE / σ(F): 1.3502924511 / Phase error: 24.8970812351 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.5473330333 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77263620528→42.2041207773 Å
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Refine LS restraints |
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LS refinement shell |
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