[English] 日本語
Yorodumi- PDB-5kji: Crystal structure of an active polycomb repressive complex 2 in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kji | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of an active polycomb repressive complex 2 in the basal state | |||||||||
Components |
| |||||||||
Keywords | TRANSFERASE / Complex / Methyltransferase | |||||||||
Function / homology | Function and homology information histone methyltransferase activity / methylation / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | |||||||||
Authors | Jiao, L. / Liu, X. | |||||||||
Citation | Journal: Science / Year: 2016 Title: Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2". Authors: Jiao, L. / Liu, X. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kji.cif.gz | 527.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kji.ent.gz | 424.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kji ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kji | HTTPS FTP |
---|
-Related structure data
Related structure data | 5kjhSC 5kklC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 S288c (yeast) / References: UniProt: G0S8H7 | ||||
---|---|---|---|---|---|
#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), (gene. exp.) Chaetomium thermophilum (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230, CTHT_0006210 / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: G0SDW4, UniProt: G0RYC6 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SAH / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.71→47.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.71→2.78 Å / Total num. of bins used: 19
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|