+Open data
-Basic information
Entry | Database: PDB / ID: 5f0n | ||||||
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Title | Cohesin subunit Pds5 | ||||||
Components | cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5,KLTH0D07062p,cohesin subunit Pds5,cohesin subunit Pds5, cohesin subunit Pds5 | ||||||
Keywords | CELL CYCLE / heat repeat cohesin subunit | ||||||
Function / homology | Sister chromatid cohesion protein Pds5 / Sister chromatid cohesion protein PDS5 protein / mitotic sister chromatid cohesion / Armadillo-like helical / Armadillo-type fold / cell division / nucleus / KLTH0D07062p Function and homology information | ||||||
Biological species | Lachancea thermotolerans (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 5f0n.cif.gz | 213.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f0n.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0n ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0n | 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: 129680.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lachancea thermotolerans (fungus), (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus) Gene: 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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, and 1.3-1.6 M lithium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9796 Å | |||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2015 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→46.67 Å / Num. obs: 28140 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.056 / Net I/σ(I): 14.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.667 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 2.83 / Phase error: 33.19 / 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: 161.27 Å2 / Biso mean: 65.4874 Å2 / Biso min: 17.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→46.667 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: 10
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