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Yorodumi- PDB-5wf7: Chaetomium thermophilum Polycomb Repressive Complex 2 bound to GSK126 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wf7 | |||||||||||||||||||||
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Title | Chaetomium thermophilum Polycomb Repressive Complex 2 bound to GSK126 | |||||||||||||||||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / transferase / epigenetics / complex / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||||||||||||||
Function / homology | Function and homology information histone H3K27 methyltransferase activity / RSC-type complex / nucleosome binding / heterochromatin formation / chromatin DNA binding / methylation / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||||||||||||||
Authors | Bratkowski, M.A. / Liu, X. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Sci Rep / Year: 2018 Title: An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors. Authors: Bratkowski, M. / Yang, X. / Liu, X. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wf7.cif.gz | 524.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wf7.ent.gz | 422.6 KB | Display | PDB format |
PDBx/mmJSON format | 5wf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wf7_validation.pdf.gz | 787.6 KB | Display | wwPDB validaton report |
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Full document | 5wf7_full_validation.pdf.gz | 812.1 KB | Display | |
Data in XML | 5wf7_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 5wf7_validation.cif.gz | 66.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/5wf7 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/5wf7 | HTTPS FTP |
-Related structure data
Related structure data | 5wfcC 5wfdC 5wg6C 5bjsS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 66021.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0S8H7 | ||||
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#2: Protein | Mass: 106869.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230, CTHT_0006210 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SDW4, UniProt: G0RYC6 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-A9G / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM sodium malonate pH 7.0, 16% PEG 3350, 43 mM 3-cyclohexyl-1-propyphosphocholine |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.495→50 Å / Num. all: 61530 / Num. obs: 61696 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.896 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 3047 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BJS Resolution: 2.5→44.14 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.05 / 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: 2.5→44.14 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.9362 Å / Origin y: -16.6111 Å / Origin z: -34.8341 Å
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Refinement TLS group | Selection details: ALL |