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Yorodumi- PDB-4bu0: Crystal structure of Rad4 BRCT1,2 in complex with a Crb2 phosphop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bu0 | ||||||
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Title | Crystal structure of Rad4 BRCT1,2 in complex with a Crb2 phosphopeptide | ||||||
Components |
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Keywords | REPLICATION / TOPBP1 / DNA DAMAGE CHECKPOINT | ||||||
Function / homology | Function and homology information SUMOylation of transcription factors / mitotic DNA damage checkpoint signaling / mitotic spindle pole body / chromatin-protein adaptor activity / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling ...SUMOylation of transcription factors / mitotic DNA damage checkpoint signaling / mitotic spindle pole body / chromatin-protein adaptor activity / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / regulation of double-strand break repair via homologous recombination / negative regulation of DNA replication / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / methylated histone binding / DNA damage checkpoint signaling / mitotic spindle / site of double-strand break / histone binding / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | SCHIZOSACCHAROMYCES POMBE (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Qu, M. / Rappas, M. / Wardlaw, C.P. / Garcia, V. / Carr, A.M. / Oliver, A.W. / Du, L.L. / Pearl, L.H. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: Phosphorylation-Dependent Assembly and Coordination of the DNA Damage Checkpoint Apparatus by Rad4(Topbp1.). Authors: Qu, M. / Rappas, M. / Wardlaw, C.P. / Garcia, V. / Ren, J.Y. / Day, M. / Carr, A.M. / Oliver, A.W. / Du, L.L. / 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 | 4bu0.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bu0.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 4bu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/4bu0 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/4bu0 | HTTPS FTP |
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-Related structure data
Related structure data | 4bmcSC 4bmdC 4bu1C C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21236.457 Da / Num. of mol.: 1 / Fragment: BRCT1,2 DOMAINS, RESIDUES 1-186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P32372 | ||||||
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#2: Protein/peptide | Mass: 1837.920 Da / Num. of mol.: 2 / Fragment: PHOSPHOPEPTIDE, RESIDUES 180-193 / Source method: obtained synthetically / Source: (synth.) SCHIZOSACCHAROMYCES POMBE (fission yeast) / References: UniProt: P87074 #3: Chemical | #4: Chemical | ChemComp-ACT / | #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: 2.9 Å3/Da / Density % sol: 57.66 % / Description: NONE |
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Crystal grow | Details: 100MM SODIUM CITRATE PH 5.6, 20% V/V ISOPROPANOL, 20% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50.92 Å / Num. obs: 47068 / % possible obs: 99.8 % / Redundancy: 3.92 % / Biso Wilson estimate: 14.98 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.25 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BMC Resolution: 1.5→45.29 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9408 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.062
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Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.155 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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