+Open data
-Basic information
Entry | Database: PDB / ID: 5f0o | ||||||
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Title | Cohesin subunit Pds5 in complex with Scc1 | ||||||
Components |
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Keywords | CELL CYCLE / heat repeat cohesin subunit | ||||||
Function / homology | Function and homology information cohesin complex / sister chromatid cohesion / mitotic sister chromatid cohesion / cell division / nucleus Similarity search - Function | ||||||
Biological species | Lachancea thermotolerans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Lee, B.-G. / Jansma, M. / Nasmyth, K. / Lowe, J. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Crystal Structure of the Cohesin Gatekeeper Pds5 and in Complex with Kleisin Scc1. Authors: Lee, B.G. / Roig, M.B. / Jansma, M. / Petela, N. / Metson, J. / Nasmyth, K. / Lowe, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f0o.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0o.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0o ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0o | 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: 125973.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The UNK residues are part of chain A, but we could not correct the exact residues due to low resolution map Source: (gene. exp.) Lachancea thermotolerans (fungus) / Gene: KLTH0D07062g,Pds5, KLTH0D07062g / Plasmid: pHis17 / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: C5DGP8 |
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#2: Protein/peptide | Mass: 2499.833 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus) References: UniProt: C5DNF8 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM sodium cacodylate pH 6.5, 1.4 - 1.6 M ammonium sulphate and 5 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→48.49 Å / Num. obs: 22568 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.06 / Net I/σ(I): 11.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→44.486 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 39.22 / 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 max: 188.21 Å2 / Biso mean: 122.8637 Å2 / Biso min: 57.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→44.486 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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