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Yorodumi- PDB-4c07: Crystal structure of M. musculus protein arginine methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c07 | |||||||||
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Title | Crystal structure of M. musculus protein arginine methyltransferase PRMT6 with CaCl2 at 1.5 Angstroms | |||||||||
Components | PROTEIN ARGININE N-METHYLTRANSFERASE 6 | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity ...histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / regulation of mitochondrion organization / histone methyltransferase activity / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / protein modification process / cellular senescence / histone binding / methylation / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | |||||||||
Authors | Bonnefond, L. / Cura, V. / Troffer-Charlier, N. / Mailliot, J. / Wurtz, J.M. / Cavarelli, J. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 Title: Functional Insights from High Resolution Structures of Mouse Protein Arginine Methyltransferase 6. Authors: Bonnefond, L. / Stojko, J. / Mailliot, J. / Troffer-Charlier, N. / Cura, V. / Wurtz, J.M. / Cianferani, S. / Cavarelli, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c07.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c07.ent.gz | 163.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c07_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
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Full document | 4c07_full_validation.pdf.gz | 427.4 KB | Display | |
Data in XML | 4c07_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4c07_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c07 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c07 | HTTPS FTP |
-Related structure data
Related structure data | 4c03C 4c04C 4c05C 4c06C 4c08C 2y1wS 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: 42321.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 | ||
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#2: Chemical | ChemComp-CA / #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: 2.62 Å3/Da / Density % sol: 53.01 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM HEPES PH 8.0, 200 MM CACL2, 12% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRERESEARCH / Detector: CCD / Date: Jul 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.44 |
Reflection | Resolution: 1.5→40.86 Å / Num. obs: 58495 / % possible obs: 98.9 % / Observed criterion σ(I): 0.8 / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.59 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 0.84 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y1W Resolution: 1.499→40.857 Å / σ(F): 1.97 / Phase error: 32.36 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.499→40.857 Å
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Refine LS restraints |
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LS refinement shell |
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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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