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Yorodumi- PDB-4m38: Crystal structure of Trypanosoma brucei protein arginine methyltr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m38 | ||||||
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Title | Crystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy and histone H4 peptide | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE SUBSTRATE / methyltransferase / TRANSFERASE-TRANSFERASE SUBSTRATE complex | ||||||
Function / homology | Function and homology information arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway ...arginine N-methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / peptidyl-arginine N-methylation / peptidyl-arginine methylation / histone arginine N-methyltransferase activity / protein-arginine N-methyltransferase activity / histone methyltransferase activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / Transferases; Transferring one-carbon groups; Methyltransferases / chromatin remodeling / protein-containing complex / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, C. / Zhu, Y. / Shi, Y. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural determinants for the strict monomethylation activity by trypanosoma brucei protein arginine methyltransferase 7. Authors: Wang, C. / Zhu, Y. / Caceres, T.B. / Liu, L. / Peng, J. / Wang, J. / Chen, J. / Chen, X. / Zhang, Z. / Zuo, X. / Gong, Q. / Teng, M. / Hevel, J.M. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m38.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m38.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 4m38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m38_validation.pdf.gz | 909.4 KB | Display | wwPDB validaton report |
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Full document | 4m38_full_validation.pdf.gz | 912.4 KB | Display | |
Data in XML | 4m38_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 4m38_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/4m38 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/4m38 | HTTPS FTP |
-Related 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: 38985.469 Da / Num. of mol.: 2 / Fragment: UNP residues 36-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: PRMT7, Tb927.7.5490 / Production host: Escherichia coli (E. coli) References: UniProt: Q582G4, Transferases; Transferring one-carbon groups; Methyltransferases #2: Protein/peptide | Mass: 2100.501 Da / Num. of mol.: 2 / Fragment: UNP residues 2-22 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 #3: Chemical | #4: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 38.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES, 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9793 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 30812 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.069 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.17 Å
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Refine LS restraints |
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