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Yorodumi- PDB-1mvh: structure of the SET domain histone lysine methyltransferase Clr4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mvh | ||||||
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Title | structure of the SET domain histone lysine methyltransferase Clr4 | ||||||
Components | Cryptic loci regulator 4 | ||||||
Keywords | TRANSFERASE / lysine methyltransferase / clr4 / set-domain | ||||||
Function / homology | Function and homology information CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase ...CLRC complex / positive regulation of pericentric heterochromatin formation / [histone H3]-lysine9 N-trimethyltransferase / mating-type region heterochromatin / [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase / histone H3K9 trimethyltransferase activity / nuclear polyadenylation-dependent antisense transcript catabolic process / histone H3K9 monomethyltransferase activity / siRNA-mediated pericentric heterochromatin formation / [histone H3]-lysine9 N-methyltransferase / ubiquitin-modified histone reader activity / chromosome, subtelomeric region / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / pericentric heterochromatin formation / protein-lysine N-methyltransferase activity / spindle pole body / silent mating-type cassette heterochromatin formation / histone methyltransferase activity / pericentric heterochromatin / histone reader activity / ubiquitin binding / methyltransferase activity / single-stranded DNA binding / methylation / double-stranded DNA binding / single-stranded RNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Min, J.R. / Zhang, X. / Cheng, X.D. / Grewal, S.I.S. / Xu, R.-M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structure of the SET domain histone lysine methyltransferase Clr4. Authors: Min, J. / Zhang, X. / Cheng, X. / Grewal, S.I. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mvh.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mvh.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mvh_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 1mvh_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 1mvh_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1mvh_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/1mvh ftp://data.pdbj.org/pub/pdb/validation_reports/mv/1mvh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33923.895 Da / Num. of mol.: 1 / Fragment: Residues 192-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Production host: Escherichia coli (E. coli) / References: UniProt: O60016 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-NI / | #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: 2.28 Å3/Da / Density % sol: 46.15 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: BRANDEIS - B1.2 / Detector: CCD / Date: Mar 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 14899 / Num. obs: 14753 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. obs: 14740 / Num. measured all: 386726 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.268 / Rfactor Rwork: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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