[English] 日本語
Yorodumi- PDB-4mvy: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mvy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea (Chem 1387) | |||||||||
Components | Methionyl-tRNA synthetaseMethionine—tRNA ligase | |||||||||
Keywords | LIGASE/LIGASE INHIBITOR / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann fold / translation / nucleotide binding / 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 (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.314 Å | |||||||||
Authors | Koh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Liu, J. / Zhang, Z. / Fan, E. / Verlinde, C.L.M.J. / Hol, W.G.J. | |||||||||
Citation | Journal: Plos Negl Trop Dis / Year: 2014 Title: Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness. Authors: Koh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Ranade, R.M. / Liu, J. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4mvy.cif.gz | 447.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4mvy.ent.gz | 365.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/4mvy ftp://data.pdbj.org/pub/pdb/validation_reports/mv/4mvy | HTTPS FTP |
---|
-Related structure data
Related structure data | 4mvwC 4mvxC 4mw0C 4mw1C 4mw2C 4mw4C 4mw5C 4mw6C 4mw7C 4mw9C 4mwbC 4mwcC 4mwdC 4mweC 4eg8S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61434.707 Da / Num. of mol.: 2 / Fragment: UNP residues 237-773 / Mutation: K456A, K457R, E458A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb10.70.6470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38C91, methionine-tRNA ligase |
---|
-Non-polymers , 5 types, 573 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-MET / | #5: Chemical | ChemComp-387 / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.65 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate, pH 6.0-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K PH range: 6.0-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010 |
Diffraction measurement | Details: 1.00 degrees, 5.0 sec, detector distance 319.94 mm |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.11 / Number: 557852 |
Reflection | Resolution: 2.314→50 Å / Num. obs: 82839 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Χ2: 0.995 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.314→2.34 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.105 / Rsym value: 0.791 / % possible all: 93.4 |
Cell measurement | Reflection used: 557852 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 33.12 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EG8 Resolution: 2.314→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.362 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.06 Å2 / Biso mean: 37.1222 Å2 / Biso min: 16.59 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.314→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|