+Open data
-Basic information
Entry | Database: PDB / ID: 5me3 | ||||||||||||
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Title | Structure of the Scc2 C-terminus | ||||||||||||
Components |
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Keywords | CELL CYCLE / cohesin loader / HEAT repeat / Scc2 | ||||||||||||
Function / homology | Function and homology information positive regulation of cohesin loading / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / replication-born double-strand break repair via sister chromatid exchange ...positive regulation of cohesin loading / Scc2-Scc4 cohesin loading complex / mitotic cohesin loading / 2-micrometer circle DNA / tRNA gene clustering / rDNA chromatin condensation / establishment of protein localization to chromatin / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / kinetochore binding / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / mitotic chromosome condensation / regulation of gene expression / sequence-specific DNA binding / chromatin binding / chromatin / cytosol Similarity search - Function | ||||||||||||
Biological species | Ashbya gossypii (fungus) Eremothecium gossypii ATCC 10895 (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.85 Å | ||||||||||||
Authors | Chao, W.C.H. / Singleton, M.R. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structure of the cohesin loader Scc2. Authors: Chao, W.C. / Murayama, Y. / Munoz, S. / Jones, A.W. / Wade, B.O. / Purkiss, A.G. / Hu, X.W. / Borg, A. / Snijders, A.P. / Uhlmann, F. / Singleton, M.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5me3.cif.gz | 412.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5me3.ent.gz | 325.3 KB | Display | PDB format |
PDBx/mmJSON format | 5me3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5me3_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 5me3_full_validation.pdf.gz | 507 KB | Display | |
Data in XML | 5me3_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 5me3_validation.cif.gz | 89 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5me3 ftp://data.pdbj.org/pub/pdb/validation_reports/me/5me3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 131560.844 Da / Num. of mol.: 2 / Fragment: UNP residues 378-1479 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (fungus) Gene: SCC2, AGL133W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q750S2 #2: Protein/peptide | | Mass: 1464.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: unassigned sequence of Scc2 Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus) Production host: Spodoptera frugiperda (fall armyworm) #3: Protein/peptide | | Mass: 2315.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Scc2 unassigned sequence Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus) Production host: Spodoptera frugiperda (fall armyworm) #4: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eremothecium gossypii ATCC 10895 (fungus) Production host: Spodoptera frugiperda (fall armyworm) |
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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: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM imidazole (pH 6.8), 200 mM lithium sulphate, and 4.5% polyethylene glycol 5000 MME |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.81 Å / Num. obs: 65853 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.0715 / Net I/σ(I): 10.36 |
Reflection shell | Resolution: 2.85→2.952 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 0.75 / CC1/2: 0.312 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.85→48.81 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9 / 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: 2.85→48.81 Å
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Refine LS restraints |
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LS refinement shell |
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