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Yorodumi- PDB-3l41: Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l41 | ||||||
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Title | Crystal Structure of S. pombe Brc1 BRCT5-BRCT6 domains in complex with phosphorylated H2A | ||||||
Components |
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Keywords | CELL CYCLE / Brc1 / BRCT domain / Tandem BRCT repeat / phosphoserine binding domain / DNA repair / Cell division / Mitosis | ||||||
Function / homology | Function and homology information DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / chromosome, subtelomeric region / chromatin-protein adaptor activity / rDNA heterochromatin / chromosome, centromeric region / double-strand break repair / site of double-strand break / DNA repair / nucleolus / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Williams, R.S. / Williams, J.S. / Guenther, G. / Tainer, J.A. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: gammaH2A binds Brc1 to maintain genome integrity during S-phase. Authors: Williams, J.S. / Williams, R.S. / Dovey, C.L. / Guenther, G. / Tainer, J.A. / Russell, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l41.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l41.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/3l41 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/3l41 | 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: 24825.396 Da / Num. of mol.: 1 / Fragment: BRCT5-BRCT6 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: brc1, SPBC582.05c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q10337 |
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#2: Protein/peptide | Mass: 781.767 Da / Num. of mol.: 1 / Fragment: phosphorylated H2A tail / Source method: obtained synthetically / Details: Synthetic peptide |
#3: 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: 2.08 Å3/Da / Density % sol: 40.83 % |
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Crystal grow | Temperature: 295 K Details: 17-20% PEG3350, 200 mM ammonium chloride, pH unk, VAPOR DIFFUSION, HANGING DROP, temperature 295K PH range: UNK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.111 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2006 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.111 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 36848 / Num. obs: 36848 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.052 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.239 / % possible all: 67.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.065 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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