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Yorodumi- PDB-5oqq: Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oqq | |||||||||
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Title | Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex | |||||||||
Components |
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Keywords | CELL CYCLE / kleisin / HEAT repeat / DNA-binding / SMC complex | |||||||||
Function / homology | Function and homology information negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation ...negative regulation of meiotic DNA double-strand break formation / meiotic chromosome condensation / Condensation of Prometaphase Chromosomes / tRNA gene clustering / meiotic chromosome separation / condensin complex / rDNA chromatin condensation / synaptonemal complex assembly / mitotic chromosome condensation / chromosome condensation / mitotic sister chromatid segregation / condensed chromosome / cell division / chromatin binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 | 5oqq.cif.gz | 678.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oqq.ent.gz | 562.6 KB | Display | PDB format |
PDBx/mmJSON format | 5oqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/5oqq ftp://data.pdbj.org/pub/pdb/validation_reports/oq/5oqq | HTTPS FTP |
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-Related structure data
Related structure data | 5oqnC 5oqoC 5oqpC 5oqrSC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 99715.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: loop deletion: 499-555 Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: YCG1, YCS5, YDR325W / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q06680 #2: Protein | Mass: 18134.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 384-529 Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: BRN1, YBL097W, YBL0830 / Plasmid: pETMCN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P38170 #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: 3.13 Å3/Da / Density % sol: 60.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 3% (w/v) PEG 4000, 0.1 M Na citrate pH 5.5 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: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→49.44 Å / Num. obs: 73424 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.046 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.79→2.94 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.745 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10633 / CC1/2: 0.444 / Rpim(I) all: 0.564 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OQR Resolution: 2.79→47.254 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.86 / 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: 2.79→47.254 Å
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Refine LS restraints |
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LS refinement shell |
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