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- PDB-5kji: Crystal structure of an active polycomb repressive complex 2 in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kji | |||||||||
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Title | Crystal structure of an active polycomb repressive complex 2 in the basal state | |||||||||
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![]() | TRANSFERASE / Complex / Methyltransferase | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Jiao, L. / Liu, X. | |||||||||
![]() | ![]() Title: Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2". Authors: Jiao, L. / 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 | ![]() | 527.4 KB | Display | ![]() |
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PDB format | ![]() | 424.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.5 KB | Display | ![]() |
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Full document | ![]() | 779.1 KB | Display | |
Data in XML | ![]() | 43.2 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kjhSC ![]() 5kklC S: Starting model for refinement C: citing same article ( |
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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: 106869.594 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_0053230, CTHT_0006210 / Production host: ![]() ![]() | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SAH / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 175mM ammonium citrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 40497 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 58.6 Å2 / Rsym value: 0.046 / Net I/σ(I): 26.18 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.72 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KJH Resolution: 2.71→47.31 Å / Cor.coef. Fo:Fc: 0.9255 / Cor.coef. Fo:Fc free: 0.8687 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.35
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Displacement parameters | Biso mean: 48.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.71→47.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.78 Å / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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