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Yorodumi- PDB-5nfh: Trypanosoma brucei methionyl-tRNA synthetase in complex with a qu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nfh | ||||||||||||
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Title | Trypanosoma brucei methionyl-tRNA synthetase in complex with a quinazolinone inhibitor | ||||||||||||
Components | Methionyl-tRNA synthetase, putativeMethionine—tRNA ligase | ||||||||||||
Keywords | LIGASE / SYNTHETASE / METHIONINE / INHIBITOR / LIGASE-LIGASE INHIBITOR / COMPLEX / DRUG DISCOVERY | ||||||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||||||||
Authors | Robinson, D.A. / Eadsforth, T.C. / Shepherd, S.M. / Torrie, L.S. / De Rycker, M. / Gilbert, I.H. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: ACS Infect Dis / Year: 2017 Title: Chemical Validation of Methionyl-tRNA Synthetase as a Druggable Target in Leishmania donovani. Authors: Torrie, L.S. / Brand, S. / Robinson, D.A. / Ko, E.J. / Stojanovski, L. / Simeons, F.R.C. / Wyllie, S. / Thomas, J. / Ellis, L. / Osuna-Cabello, M. / Epemolu, O. / Nuhs, A. / Riley, J. / ...Authors: Torrie, L.S. / Brand, S. / Robinson, D.A. / Ko, E.J. / Stojanovski, L. / Simeons, F.R.C. / Wyllie, S. / Thomas, J. / Ellis, L. / Osuna-Cabello, M. / Epemolu, O. / Nuhs, A. / Riley, J. / MacLean, L. / Manthri, S. / Read, K.D. / Gilbert, I.H. / Fairlamb, A.H. / De Rycker, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nfh.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nfh.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/5nfh ftp://data.pdbj.org/pub/pdb/validation_reports/nf/5nfh | HTTPS FTP |
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-Related structure data
Related structure data | 4egaS S: Starting model for refinement |
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Similar 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60669.031 Da / Num. of mol.: 2 / Mutation: K452A, K453R, E454A 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 |
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-Non-polymers , 5 types, 273 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-MET / | #5: Chemical | ChemComp-8W2 / | #6: 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: 3.93 Å3/Da / Density % sol: 68.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 2.0-2.3 M Ammonium Sulphate, 0.2 M NaCl, 0.1 M Na Cacodylate pH 6.4 PH range: 6.0-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014 | |||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 47875 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.082 / Rrim(I) all: 0.176 / Net I/σ(I): 9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EGA Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.895 / SU ML: 0.24 / SU R Cruickshank DPI: 0.5035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.504 / ESU R Free: 0.288 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 162.18 Å2 / Biso mean: 45.056 Å2 / Biso min: 10.18 Å2
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Refinement step | Cycle: final / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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