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- PDB-5tqr: ctPRC2 in an autoinhibited conformation bound to S-adenosylmethionine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tqr | |||||||||||||||||||||
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Title | ctPRC2 in an autoinhibited conformation bound to S-adenosylmethionine | |||||||||||||||||||||
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![]() | TRANSFERASE | |||||||||||||||||||||
Function / homology | ![]() histone H3K27 methyltransferase activity / ESC/E(Z) complex / RSC-type complex / heterochromatin formation / nucleosome binding / chromatin DNA binding / methylation / chromatin binding / negative regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Bratkowski, M.A. / Liu, X. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Polycomb repressive complex 2 in an autoinhibited state. Authors: Bratkowski, M. / Yang, X. / Liu, X. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 548.1 KB | Display | ![]() |
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PDB format | ![]() | 439.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.2 KB | Display | ![]() |
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Full document | ![]() | 834 KB | Display | |
Data in XML | ![]() | 47.6 KB | Display | |
Data in CIF | ![]() | 67.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bjsSC ![]() 5vk3C 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 on special symmetry positions |
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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.) ![]() ![]() ![]() | ||||
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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.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SAM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.02 % |
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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-propylphosphocholine |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 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: 2.57→50 Å / Num. obs: 55206 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 61.82 Å2 / CC1/2: 0.89 / Rmerge(I) obs: 0.162 / Net I/σ(I): 12.79 |
Reflection shell | Resolution: 2.57→2.61 Å / Redundancy: 9 % / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.63 / CC1/2: 0.552 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BJS Resolution: 2.571→47.322 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.97 / 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: 2.571→47.322 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: 22.7986 Å / Origin y: 17.7375 Å / Origin z: -35.0451 Å
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Refinement TLS group | Selection details: all |