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Yorodumi- PDB-3vv0: Crystal structure of histone methyltransferase SET7/9 in complex ... -
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-Basic information
Entry | Database: PDB / ID: 3vv0 | ||||||
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Title | Crystal structure of histone methyltransferase SET7/9 in complex with DAAM-3 | ||||||
Components | Histone-lysine N-methyltransferase SETD7 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SET domain / transferase / adenosylmethionine binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / heterochromatin organization / PKMTs methylate histone lysines / p53 binding ...peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / histone methyltransferase activity / heterochromatin organization / PKMTs methylate histone lysines / p53 binding / chromatin organization / chromosome / response to ethanol / DNA damage response / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Niwa, H. / Handa, N. / Tomabechi, Y. / Honda, K. / Toyama, M. / Ohsawa, N. / Shirouzu, M. / Kagechika, H. / Hirano, T. / Umehara, T. / Yokoyama, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives Authors: Niwa, H. / Handa, N. / Tomabechi, Y. / Honda, K. / Toyama, M. / Ohsawa, N. / Shirouzu, M. / Kagechika, H. / Hirano, T. / Umehara, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vv0.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vv0.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vv0_validation.pdf.gz | 703.2 KB | Display | wwPDB validaton report |
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Full document | 3vv0_full_validation.pdf.gz | 704.1 KB | Display | |
Data in XML | 3vv0_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3vv0_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/3vv0 ftp://data.pdbj.org/pub/pdb/validation_reports/vv/3vv0 | HTTPS FTP |
-Related structure data
Related structure data | 3vuzC 1n6aS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29083.244 Da / Num. of mol.: 1 / Fragment: residues 111-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: PX100709-08 / Production host: CELL-FREE SYNTHESIS (others) References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-KH3 / |
#3: 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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-HCl pH8.3-8.5, 28-30% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K PH range: 8.3-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 24, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 18855 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 33.37 Å2 / Rsym value: 0.081 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.718 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1n6a Resolution: 2.001→28.176 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 1.33 / Phase error: 20.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.86 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.32 Å2 / Biso mean: 47.0282 Å2 / Biso min: 17.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→28.176 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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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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