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Yorodumi- PDB-5vah: Crystal structure of ATXR5 SET domain in complex with histone H3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vah | |||||||||
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Title | Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26 | |||||||||
Components |
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Keywords | TRANSFERASE/DNA BINDING PROTEIN / histone / nucleosome / methyltransferases / TRANSFERASE-DNA BINDING PROTEIN complex | |||||||||
Function / homology | Function and homology information [histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / histone acetyltransferase activity / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation ...[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / histone acetyltransferase activity / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Ricinus communis (castor bean) Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. ...Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.-F. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Molecular basis for the methylation specificity of ATXR5 for histone H3. Authors: Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M.S. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vah.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vah.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vah_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5vah_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5vah_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 5vah_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/5vah ftp://data.pdbj.org/pub/pdb/validation_reports/va/5vah | HTTPS FTP |
-Related structure data
Related structure data | 5va6C 5vabC 5vacC 5vbcC 4o30S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26218.723 Da / Num. of mol.: 2 / Fragment: residues 146-374 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Gene: ATXR5, RCOM_1460410 / Production host: Escherichia coli (E. coli) References: UniProt: B9RU15, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1415.637 Da / Num. of mol.: 2 / Fragment: residues 22-36 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→17 Å / Num. obs: 19507 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.13 Å2 / Rsym value: 0.061 / Net I/σ(I): 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O30 Resolution: 2.4→16.93 Å / Cor.coef. Fo:Fc: 0.9112 / Cor.coef. Fo:Fc free: 0.8798 / SU R Cruickshank DPI: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.475 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.291
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Displacement parameters | Biso mean: 37.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→16.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.53 Å / Total num. of bins used: 10
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