+Open data
-Basic information
Entry | Database: PDB / ID: 5oqr | |||||||||
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Title | Crystal structure of the S. pombe condensin Cnd3-Cnd2 subcomplex | |||||||||
Components |
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Keywords | CELL CYCLE / kleisin / HEAT repeat / DNA-binding / SMC complex | |||||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activator activity / Condensation of Prometaphase Chromosomes / CENP-A containing chromatin / DNA topoisomerase binding / condensin complex / rDNA heterochromatin / attachment of mitotic spindle microtubules to kinetochore / mitotic chromosome condensation / heterochromatin / condensed chromosome ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activator activity / Condensation of Prometaphase Chromosomes / CENP-A containing chromatin / DNA topoisomerase binding / condensin complex / rDNA heterochromatin / attachment of mitotic spindle microtubules to kinetochore / mitotic chromosome condensation / heterochromatin / condensed chromosome / cell division / DNA repair / chromatin binding / chromatin / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | |||||||||
Authors | Kschonsak, M. / Hassler, M. / Haering, C.H. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Cell / Year: 2017 Title: Structural Basis for a Safety-Belt Mechanism That Anchors Condensin to Chromosomes. Authors: Kschonsak, M. / Merkel, F. / Bisht, S. / Metz, J. / Rybin, V. / Hassler, M. / Haering, C.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oqr.cif.gz | 608.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oqr.ent.gz | 511 KB | Display | PDB format |
PDBx/mmJSON format | 5oqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oqr_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 5oqr_full_validation.pdf.gz | 488 KB | Display | |
Data in XML | 5oqr_validation.xml.gz | 52.9 KB | Display | |
Data in CIF | 5oqr_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/5oqr ftp://data.pdbj.org/pub/pdb/validation_reports/oq/5oqr | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 90813.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: loop deletion: 439-473 Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: cnd3, SPCC188.03 / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q10429 #2: Protein | Mass: 15606.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 416-544 Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: cnd2, SPCC306.03c / Plasmid: pETMCN / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q9Y7R3 #3: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion Details: 3 to 4% (w/v) PEG 4000, 0.1 M Na citrate pH 5.2 to 5.4, 0.2 M Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→49.06 Å / Num. obs: 68083 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.06 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.61→2.67 Å / Redundancy: 13 % / Rmerge(I) obs: 1.482 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4542 / CC1/2: 0.678 / Rpim(I) all: 0.425 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→49.059 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→49.059 Å
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Refine LS restraints |
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LS refinement shell |
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