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Yorodumi- PDB-5j5a: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j5a | ||||||
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Title | Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (Chem 70786556) | ||||||
Components | Methionyl-tRNA synthetase, putativeMethionine—tRNA ligase | ||||||
Keywords | Ligase/Ligase Inhibitor / synthetase / ligase / methionine / inhibitor / Ligase-Ligase Inhibitor complex | ||||||
Function / homology | Function and homology information methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Barros-Alvarez, X. / Koh, C.Y. / Hol, W.G.J. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2016 Title: Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors. Authors: Huang, W. / Zhang, Z. / Barros-Alvarez, X. / Koh, C.Y. / Ranade, R.M. / Gillespie, J.R. / Creason, S.A. / Shibata, S. / Verlinde, C.L. / Hol, W.G. / Buckner, F.S. / Fan, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j5a.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j5a.ent.gz | 174.5 KB | Display | PDB format |
PDBx/mmJSON format | 5j5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/5j5a ftp://data.pdbj.org/pub/pdb/validation_reports/j5/5j5a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 238 - 767 / Label seq-ID: 7 - 536
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-Components
#1: Protein | Mass: 61330.715 Da / Num. of mol.: 2 / Mutation: A309T, K452A, K453R, E454A, A499V, S503N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38C91, methionine-tRNA ligase #2: Chemical | ChemComp-MET / | #3: Chemical | ChemComp-756 / [( | #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: 3.91 Å3/Da / Density % sol: 68.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 1.8-2.1 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate, pH 6.2-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37.9 Å / Num. obs: 53600 / % possible obs: 99.8 % / Redundancy: 5.1 % / Net I/σ(I): 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→37.69 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: FREE R-VALUE / ESU R: 0.425 / ESU R Free: 0.273 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.051 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→37.69 Å
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Refine LS restraints |
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