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- PDB-4c08: Crystal structure of M. musculus protein arginine methyltransfera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c08 | |||||||||
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Title | Crystal structure of M. musculus protein arginine methyltransferase PRMT6 with CaCl2 at 1.34 Angstroms | |||||||||
![]() | PROTEIN ARGININE N-METHYLTRANSFERASE 6 | |||||||||
![]() | TRANSFERASE / S-ADENOSYL-L-METHIONINE | |||||||||
Function / homology | ![]() histone H2AR3 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / histone H4R3 methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bonnefond, L. / Cura, V. / Troffer-Charlier, N. / Mailliot, J. / Wurtz, J.M. / Cavarelli, J. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.4 KB | Display | ![]() |
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PDB format | ![]() | 169.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 434.2 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c03C ![]() 4c04C ![]() 4c05C ![]() 4c06C ![]() 4c07C ![]() 2y1wS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() ![]() References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 | ||
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#2: Chemical | ChemComp-1PE / | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM TRIS PH 8.0, 200 MM CACL2, 19% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→33.98 Å / Num. obs: 81559 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Biso Wilson estimate: 19.81 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.99 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.2 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y1W Resolution: 1.338→33.983 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 15.98 / Stereochemistry target values: ML
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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: 1.338→33.983 Å
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Refine LS restraints |
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LS refinement shell |
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