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Yorodumi- PDB-5upd: Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5upd | |||||||||
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Title | Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1) | |||||||||
Components | Histone-lysine N-methyltransferase NSD3 | |||||||||
Keywords | TRANSFERASE / Structural Genomics Consortium / methyl transferase / SGC | |||||||||
Function / homology | Function and homology information [histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Tempel, W. / Yu, W. / Dong, A. / Cerovina, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To Be Published Title: Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1) Authors: Tempel, W. / Yu, W. / Dong, A. / Cerovina, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5upd.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5upd.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 5upd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5upd ftp://data.pdbj.org/pub/pdb/validation_reports/up/5upd | HTTPS FTP |
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-Related structure data
Related structure data | 3ooiS 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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Details | AUTHOR-DETERMINED QUATERNARY STRUCTURE: not available |
-Components
#1: Protein | Mass: 26494.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WHSC1L1, NSD3, DC28 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRARE-V2R References: UniProt: Q9BZ95, histone-lysine N-methyltransferase | ||||
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#2: Chemical | ChemComp-SAM / | ||||
#3: Chemical | ChemComp-UNX / #4: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.87 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 29, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97957 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→41.55 Å / Num. obs: 23067 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.064 / Rrim(I) all: 0.124 / Net I/σ(I): 11.1 / Num. measured all: 85056 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3OOI Resolution: 1.8→41.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.051 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ARP/WARP was used for automated model building. COOT was used for interactive model building. PHENIX.MOLPROBITY was used for validation of model geometry
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.29 Å2 / Biso mean: 24.398 Å2 / Biso min: 9.58 Å2
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Refinement step | Cycle: final / Resolution: 1.8→41.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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