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Yorodumi- PDB-3oxf: Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form I) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oxf | ||||||
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Title | Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form I) | ||||||
Components | SET and MYND domain-containing protein 3 | ||||||
Keywords | TRANSFERASE / Smyd proteins / MYND / SET domain / histone lysine methyltransferase / histone methylation / H3K4 | ||||||
Function / homology | Function and homology information histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | ||||||
Authors | Xu, S. / Wu, J. / Sun, B. / Zhong, C. / Ding, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding. Authors: Xu, S. / Wu, J. / Sun, B. / Zhong, C. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oxf.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oxf.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 3oxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/3oxf ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3oxf | HTTPS FTP |
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-Related structure data
Related structure data | 3oxgC 3oxlC 3mekS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50249.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus References: UniProt: Q9H7B4, histone-lysine N-methyltransferase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Sequence details | THE EXPERIMENTAL INFO OF UNIPROT (Q9H7B4, SMYD3_HUMAN) SHOWS CONFLICTS K -> N, K -> R AT THE ...THE EXPERIMENT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14.4% PEG 8000, 20% glycerol, 160mM calcium acetate, and 80mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 4, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 26338 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.122 / Χ2: 1.015 / Net I/av σ(I): 9.832 / Net I/σ(I): 7.6 / Num. measured all: 86956 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MEK Resolution: 2.82→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.37 Å2 / Biso mean: 40.2781 Å2 / Biso min: 9.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.815→2.888 Å / Total num. of bins used: 20
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