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Yorodumi- PDB-8bva: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bva | ||||||
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Title | Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_114-126 | ||||||
Components |
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Keywords | TRANSFERASE / protein arginine N-methyltransferase / PRMT / SH3 / methylation / TRANSCRIPTION | ||||||
Function / homology | Function and homology information protein-arginine N-methyltransferase activity / methylation / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Spodoptera aff. frugiperda 2 BOLD-2017 (butterflies/moths) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Cura, V. / Troffer-Charlier, N. / Marechal, N. / Bonnefond, L. / Cavarelli, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_114-126 Authors: Cura, V. / Troffer-Charlier, N. / Marechal, N. / 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 | 8bva.cif.gz | 257.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bva.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bva_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 8bva_full_validation.pdf.gz | 760.3 KB | Display | |
Data in XML | 8bva_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 8bva_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bva ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bva | HTTPS FTP |
-Related structure data
Related structure data | 5fulS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 39067.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prmt2, Hrmt1l1 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q3UKX1 |
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#2: Protein/peptide | Mass: 1470.510 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Spodoptera aff. frugiperda 2 BOLD-2017 (butterflies/moths) References: UniProt: A0A2H1V327 |
-Non-polymers , 4 types, 88 molecules
#3: Chemical | ChemComp-TLA / |
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#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-QVR / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2M ammonium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→29.55 Å / Num. obs: 25946 / % possible obs: 99.1 % / Redundancy: 13.8 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.11 / Χ2: 1 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.19→2.26 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.48 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2056 / CC1/2: 0.686 / Rrim(I) all: 1.541 / Χ2: 0.97 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FUL Resolution: 2.19→29.55 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.124 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 54.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→29.55 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 | Refine-ID: X-RAY DIFFRACTION
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