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Yorodumi- PDB-5fqn: Crystal structure of M. musculus protein arginine methyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fqn | ||||||
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Title | Crystal structure of M. musculus protein arginine methyltransferase PRMT6 with SAH at 1.65 Angstroms | ||||||
Components | PROTEIN ARGININE METHYLTRANSFERASE 6 | ||||||
Keywords | TRANSFERASE / S-ADENOSYL-L-METHIONINE | ||||||
Function / homology | Function and homology information 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 | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.657 Å | ||||||
Authors | Bonnefond, L. / Cavarelli, J. | ||||||
Citation | Journal: To be Published Title: Crystal Strcutures of Prmt6 in Complex with Sah in Alternative Conformations Authors: Bonnefond, L. / Cura, V. / Troffer-Charlier, N. / Cavarelli, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fqn.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fqn.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fqn_validation.pdf.gz | 962.5 KB | Display | wwPDB validaton report |
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Full document | 5fqn_full_validation.pdf.gz | 966.1 KB | Display | |
Data in XML | 5fqn_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 5fqn_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fqn ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fqn | HTTPS FTP |
-Related structure data
Related structure data | 5fqoC 4c08S 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: 44355.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PNEA-VH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6NZB1, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 |
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#2: Chemical | ChemComp-SAH / |
#3: Water | ChemComp-HOH / |
Sequence details | L315P NATURAL VARIANT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM TRIS PH 8.0 200 MM MGCL2 12% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2015 Details: A CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK- BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40.8 Å / Num. obs: 43482 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 0.8 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C08 Resolution: 1.657→40.772 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 23.61 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.657→40.772 Å
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Refine LS restraints |
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LS refinement shell |
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