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Yorodumi- PDB-5frp: Structure of the Pds5-Scc1 complex and implications for cohesin f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5frp | |||||||||
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Title | Structure of the Pds5-Scc1 complex and implications for cohesin function | |||||||||
Components |
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Keywords | CELL CYCLE / CELL DIVISION / COHESIN / DNA REPLICATION / SISTER CHROMATID COHESION / PDS5 / SMC3 / SCC1 / SMC1 / WAPL | |||||||||
Function / homology | Function and homology information meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic DNA double-strand break formation / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / homologous chromosome pairing at meiosis / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion ...meiotic recombination initiation complex / Establishment of Sister Chromatid Cohesion / Resolution of Sister Chromatid Cohesion / meiotic DNA double-strand break formation / mitotic cohesin complex / cohesin complex / SUMOylation of DNA damage response and repair proteins / homologous chromosome pairing at meiosis / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / mitotic chromosome condensation / mitotic sister chromatid cohesion / protein acetylation / chromosome, centromeric region / meiotic cell cycle / condensed nuclear chromosome / double-strand break repair / cell division / apoptotic process / DNA damage response / chromatin binding / chromatin / protein kinase binding / structural molecule activity / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.895 Å | |||||||||
Authors | Muir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D. | |||||||||
Citation | Journal: Cell Rep. / Year: 2016 Title: Structure of the Pds5-Scc1 Complex and Implications for Cohesin Function Authors: Muir, K.W. / Kschonsak, M. / Li, Y. / Metz, J. / Haering, C.H. / Panne, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5frp.cif.gz | 518.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5frp.ent.gz | 435.9 KB | Display | PDB format |
PDBx/mmJSON format | 5frp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5frp ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5frp | 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 80738.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04264 #2: Protein/peptide | Mass: 4955.659 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q12158 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 100 |
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-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.76 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 59992 / % possible obs: 96.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.58 % / Biso Wilson estimate: 88.35 Å2 / Rmerge(I) obs: 0.5 / Net I/σ(I): 9.14 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.895→48.22 Å / SU ML: 0.53 / σ(F): 0.11 / Phase error: 35.85 / Stereochemistry target values: ML
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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: 106 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.895→48.22 Å
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Refine LS restraints |
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LS refinement shell |
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