+Open data
-Basic information
Entry | Database: PDB / ID: 4bmd | ||||||
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Title | Crystal structure of S.pombe Rad4 BRCT3,4 | ||||||
Components | S-M CHECKPOINT CONTROL PROTEIN RAD4 | ||||||
Keywords | REPLICATION / TOPBP1 / BRCT / DNA DAMAGE CHECKPOINT | ||||||
Function / homology | Function and homology information mitotic DNA damage checkpoint signaling / mitotic spindle pole body / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / mitotic spindle / site of double-strand break ...mitotic DNA damage checkpoint signaling / mitotic spindle pole body / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / DNA replication initiation / signaling adaptor activity / 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: 2.5 Å | ||||||
Authors | Meng, Q. / 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 | 4bmd.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bmd.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bmd ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bmd | HTTPS FTP |
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-Related structure data
Related structure data | 4bmcC 4bu0C 4bu1C 2xnhS 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
#1: Protein | Mass: 23738.248 Da / Num. of mol.: 1 / Fragment: BRCT3 AND BRCT4 DOMAINS, RESIDUES 291-494 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: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-MES / |
#4: 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: 3.97 Å3/Da / Density % sol: 69 % Description: BALBES SELECTED PDB ENTRY 2XNH AS THE BEST STARTING MODEL. |
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Crystal grow | Details: 0.1 M MES PH 6.5, 0.2 M NACL, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→55.05 Å / Num. obs: 13128 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.46 % / Biso Wilson estimate: 41.25 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.79 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 0.85 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XNH Resolution: 2.5→55.048 Å / SU ML: 0.36 / σ(F): 0.8 / Phase error: 21.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.732 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→55.048 Å
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Refine LS restraints |
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LS refinement shell |
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