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Yorodumi- PDB-1mt6: Structure of histone H3 K4-specific methyltransferase SET7/9 with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mt6 | ||||||
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Title | Structure of histone H3 K4-specific methyltransferase SET7/9 with AdoHcy | ||||||
Components | SET9 | ||||||
Keywords | TRANSFERASE / SET domain / histone lysine methyltransferase / AdoHcy / knot | ||||||
Function / homology | Function and homology information heterochromatin organization / 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 / PKMTs methylate histone lysines / p53 binding ...heterochromatin organization / 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 / PKMTs methylate histone lysines / p53 binding / chromosome / chromatin organization / response to ethanol / chromatin binding / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jacobs, S.A. / Harp, J.M. / Devarakonda, S. / Kim, Y. / Rastinejad, F. / Khorasanizadeh, S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: The active site of the SET domain is constructed on a knot Authors: Jacobs, S.A. / Harp, J.M. / Devarakonda, S. / Kim, Y. / Rastinejad, F. / Khorasanizadeh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mt6.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mt6.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mt6_validation.pdf.gz | 822.8 KB | Display | wwPDB validaton report |
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Full document | 1mt6_full_validation.pdf.gz | 847.1 KB | Display | |
Data in XML | 1mt6_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1mt6_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mt6 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mt6 | 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: 31150.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGex / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#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: 3.57 Å3/Da / Density % sol: 65.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, sodium citrate, Isopropanol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 17-ID / Wavelength: 0.9778 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2002 |
Radiation | Monochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 21496 / Num. obs: 21496 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.8 Å2 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 77.1 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 77.1 % / Redundancy: 2.5 % / Num. unique obs: 1768 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.64 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 132634.4 / Data cutoff high rms absF: 132634.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.6341 Å2 / ksol: 0.330675 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→28.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.225 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.356 / Rfactor Rwork: 0.37 |