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- PDB-5wfd: Humanized mutant of the Chaetomium thermophilum Polycomb Repressi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wfd | |||||||||||||||||||||
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Title | Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK126 | |||||||||||||||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / transferase / inhibitor / complex / epigenetics / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||||||||||||||
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: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 519.4 KB | Display | ![]() |
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PDB format | ![]() | 419.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.3 KB | Display | ![]() |
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Full document | ![]() | 797.6 KB | Display | |
Data in XML | ![]() | 44.3 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wf7C ![]() 5wfcC ![]() 5wg6C ![]() 5bjsS 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: 66021.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 106801.656 Da / Num. of mol.: 1 / Mutation: P302I, R304Y, E850K, N851Y, K852M, V853C, Y855F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230, CTHT_0006210 / Production host: ![]() ![]() | ||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-A9G / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.74 % / Description: Plate |
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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 S 6M / Detector: PIXEL / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.654→50 Å / Num. obs: 52188 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.882 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.066 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.654→2.7 Å / Redundancy: 11.1 % / Rmerge(I) obs: 3.146 / Num. unique obs: 2541 / CC1/2: 0.535 / Rpim(I) all: 0.975 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BJS Resolution: 2.654→46.146 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5 / 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: 2.654→46.146 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: 22.5816 Å / Origin y: 17.9179 Å / Origin z: -35.2824 Å
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Refinement TLS group | Selection details: ALL |