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- PDB-5oqo: Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oqo | |||||||||
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Title | Crystal structure of the S. cerevisiae condensin Ycg1-Brn1 subcomplex bound to DNA (crystal form II) | |||||||||
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![]() | CELL CYCLE / kleisin / HEAT repeat / DNA-binding / SMC complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kschonsak, M. / Hassler, M. / Haering, C.H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 396.7 KB | Display | ![]() |
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PDB format | ![]() | 318.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.7 KB | Display | ![]() |
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Full document | ![]() | 490.4 KB | Display | |
Data in XML | ![]() | 32.5 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oqnC ![]() 5oqpSC ![]() 5oqqC ![]() 5oqrC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 99715.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: loop deletion: 499-555 Source: (gene. exp.) ![]() ![]() Gene: YCG1, YCS5, YDR325W / Plasmid: pETMCN / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 18134.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 384-529 Source: (gene. exp.) ![]() ![]() Gene: BRN1, YBL097W, YBL0830 / Plasmid: pETMCN / Production host: ![]() ![]() | ||||
#3: DNA chain | Mass: 5515.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #5: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.93 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion Details: 5% (w/v) PEG 4000 0.05 M Na cacodylate pH 6.8 10 mM BaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→49.21 Å / Num. obs: 26286 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.113 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.854 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3796 / CC1/2: 0.513 / Rpim(I) all: 0.767 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OQP Resolution: 3.25→47.317 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.31 / 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: 3.25→47.317 Å
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Refine LS restraints |
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LS refinement shell |
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