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- PDB-4mvw: Trypanosoma brucei methionyl-tRNA synthetase in complex with inhi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mvw | |||||||||
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Title | Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433) | |||||||||
![]() | Methionyl-tRNA synthetase | |||||||||
![]() | LIGASE/LIGASE INHIBITOR / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann fold / translation / nucleotide binding / LIGASE-LIGASE INHIBITOR complex | |||||||||
Function / homology | ![]() methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ciliary plasm / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 442.2 KB | Display | ![]() |
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PDB format | ![]() | 360.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mvxC ![]() 4mvyC ![]() 4mw0C ![]() 4mw1C ![]() 4mw2C ![]() 4mw4C ![]() 4mw5C ![]() 4mw6C ![]() 4mw7C ![]() 4mw9C ![]() 4mwbC ![]() 4mwcC ![]() 4mwdC ![]() 4mweC ![]() 4eg8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 61538.684 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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 283 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/43E.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/43E.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-MET / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-43E / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.62 % |
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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 |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 23, 2010 |
Diffraction measurement | Details: 0.50 degrees, 90.0 sec, detector distance 70.00 mm |
Radiation | Monochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.202 / Number: 290946 |
Reflection | Resolution: 2.901→50 Å / Num. obs: 43617 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.202 / Rsym value: 0.202 / Χ2: 1.067 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.901→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.058 / Rsym value: 0.831 / % possible all: 100 |
Cell measurement | Reflection used: 290946 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 33.66 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4EG8 Resolution: 2.901→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.193 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 25.502 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.342 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.51 Å2 / Biso mean: 43.0186 Å2 / Biso min: 7.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.901→30 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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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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