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Yorodumi- PDB-8c1j: Crystal Structure of Mus musculus Protein Arginine Methyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c1j | ||||||
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Title | Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 in complex with RSF1_18-30 | ||||||
Components |
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Keywords | TRANSFERASE / protein arginine N-methyltransferase / PRMT / SH3 / methylation / TRANSCRIPTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_18-30 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 | 8c1j.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c1j.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/8c1j ftp://data.pdbj.org/pub/pdb/validation_reports/c1/8c1j | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
#1: Protein | Mass: 40623.246 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: 1660.823 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
#3: Chemical | ChemComp-QVR / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.1M ammonium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.69 Å / Num. obs: 34584 / % possible obs: 99.6 % / Redundancy: 26.7 % / Biso Wilson estimate: 48.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.019 / Rrim(I) all: 0.101 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 23.1 % / Rmerge(I) obs: 3.41 / Mean I/σ(I) obs: 1 / Num. unique obs: 2361 / CC1/2: 0.399 / Rpim(I) all: 0.708 / Rrim(I) all: 3.488 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.69 Å / SU ML: 0.2375 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1141 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 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.69 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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