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Yorodumi- PDB-5ful: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ful | ||||||
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Title | Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with SAH | ||||||
Components | PROTEIN ARGININE N-METHYLTRANSFERASE 2 | ||||||
Keywords | TRANSFERASE / S-ADENOSYL-L-METHIONINE / S-ADENOSYL-L-HOMOCYSTEINE | ||||||
Function / homology | Function and homology information protein-arginine N-methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J. | ||||||
Citation | Journal: FEBS J. / Year: 2017 Title: Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. Authors: Cura, V. / Marechal, N. / Troffer-Charlier, N. / Strub, J.M. / van Haren, M.J. / Martin, N.I. / Cianferani, S. / Bonnefond, L. / Cavarelli, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ful.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ful.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ful.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ful_validation.pdf.gz | 749.3 KB | Display | wwPDB validaton report |
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Full document | 5ful_full_validation.pdf.gz | 751.1 KB | Display | |
Data in XML | 5ful_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5ful_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/5ful ftp://data.pdbj.org/pub/pdb/validation_reports/fu/5ful | HTTPS FTP |
-Related structure data
Related structure data | 5fubSC 5fwaC 5fwdC 5g02C 5jmqC 5k8vC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50636.277 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q3UKX1, EC: 2.1.1.125 |
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-Non-polymers , 6 types, 316 molecules
#2: Chemical | ChemComp-SAH / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | G0 COMES FROM THE TEV CLEAVAGE SITE. MUTATION R445W |
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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 16% PEG6000, 100MM CACL2, 100MM HEPES PH7.0 |
-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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→43.6 Å / Num. obs: 40535 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FUB Resolution: 1.89→43.26 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 19.91 / Stereochemistry target values: ML / Details: RESIDUES 1-106 ARE DISORDERED.
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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: 37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→43.26 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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