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Yorodumi- PDB-7p0l: Crystal structure of S.pombe Mdb1 BRCT domains in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p0l | |||||||||
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Title | Crystal structure of S.pombe Mdb1 BRCT domains in complex with a H2A phosphopeptide | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / DNA damage response | |||||||||
Function / homology | Function and homology information mating-type region heterochromatin / heterochromatin formation => GO:0031507 / mitotic DNA damage checkpoint signaling / mitotic spindle midzone / chromosome, subtelomeric region / chromatin-protein adaptor activity / rDNA heterochromatin / mitotic chromosome condensation / mitotic G2 DNA damage checkpoint signaling / pericentric heterochromatin ...mating-type region heterochromatin / heterochromatin formation => GO:0031507 / mitotic DNA damage checkpoint signaling / mitotic spindle midzone / chromosome, subtelomeric region / chromatin-protein adaptor activity / rDNA heterochromatin / mitotic chromosome condensation / mitotic G2 DNA damage checkpoint signaling / pericentric heterochromatin / nucleosome / site of double-strand break / chromatin organization / protein heterodimerization activity / DNA repair / DNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Day, M. / Oliver, A.W. / Pearl, L.H. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: DNA Repair (Amst) / Year: 2021 Title: Phosphorylation-dependent assembly of DNA damage response systems and the central roles of TOPBP1. Authors: Day, M. / Oliver, A.W. / Pearl, L.H. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p0l.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0l.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 7p0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0l ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0l | HTTPS FTP |
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-Related structure data
Related structure data | 7p0jSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 387 - 581 / Label seq-ID: 5 - 199
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-Components
#1: Protein | Mass: 22696.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: mdb1, SPAC2E11.14, SPACUNK4.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14079 #2: Protein/peptide | Mass: 1241.246 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) References: UniProt: P04910 #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 200mM Magnesium Chloride 100mM TRIS pH 8.0 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97957 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→48.12 Å / Num. obs: 23405 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 35.94 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 1.087 |
Reflection shell | Resolution: 1.97→2.02 Å / Num. unique obs: 1720 / Rpim(I) all: 0.383 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7P0J Resolution: 1.97→48.12 Å / SU ML: 0.2648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0307 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: 48.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→48.12 Å
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Refine LS restraints |
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LS refinement shell |
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