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Yorodumi- PDB-5eku: Crystal Structure of Trypanosoma Brucei Protein Arginine Methyltr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eku | ||||||
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Title | Crystal Structure of Trypanosoma Brucei Protein Arginine Methyltransferase PRMT7 in complex with S-Adenosyl-L-homocysteine | ||||||
Components | Arginine N-methyltransferase, putative | ||||||
Keywords | TRANSFERASE / Methyltransferase / complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.801 Å | ||||||
Authors | Debler, E.W. / Stavropoulos, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: A glutamate/aspartate switch controls product specificity in a protein arginine methyltransferase. Authors: Debler, E.W. / Jain, K. / Warmack, R.A. / Feng, Y. / Clarke, S.G. / Blobel, G. / Stavropoulos, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eku.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eku.ent.gz | 242 KB | Display | PDB format |
PDBx/mmJSON format | 5eku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/5eku ftp://data.pdbj.org/pub/pdb/validation_reports/ek/5eku | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Dimer confirmed by gel filtration, multi-angle light scattering |
-Components
#1: Protein | Mass: 44083.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb427.07.5490 / Production host: Escherichia coli (E. coli) / References: UniProt: D6XJ80 #2: Chemical | Sequence details | Uniprot does not contain a reference sequence for this strain. The conflicts are relative to the ...Uniprot does not contain a reference sequence for this strain. The conflicts are relative to the closest entry. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 400, magnesium chloride, tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 34602 / % possible obs: 99.97 % / Redundancy: 5.8 % / Rsym value: 0.096 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.801→45.866 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→45.866 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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