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- PDB-9qdj: CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9qdj | ||||||
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Title | CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911 | ||||||
![]() | Lysine--tRNA ligase 1 | ||||||
![]() | LIGASE / inhibitor | ||||||
Function / homology | ![]() lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dawson, A. / Cleghorn, L.A.T. / Davis, S.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis. Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. ...Authors: Davis, S.H. / Mathieson, M. / Buchanan, K.I. / Dawson, A. / Smith, A. / Cocco, M. / Tamaki, F.K. / Post, J.M. / Baragana, B. / Jansen, C. / Kiczun, M. / Zuccotto, F. / Wood, G. / Scullion, P. / Ray, P.C. / Epemolu, O. / Lopez-Roman, E.M. / Lopez, L.G. / Engelhart, C.A. / Kim, J. / Pino, P.A. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / Green, S.R. / Cleghorn, L.A.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.5 KB | Display | ![]() |
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Full document | ![]() | 783.4 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9qbrC ![]() 9qc3C ![]() 9qc4C ![]() 9qeaC ![]() 9qeiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58189.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LYS / |
#3: Chemical | ChemComp-A1I60 / Mass: 298.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16F2N4O2 / Feature type: SUBJECT OF INVESTIGATION |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % / Description: block |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: reservoir: 0.25 M NaOAc, 14% W/V PEG 3350 Protein buffer: 25 mM HEPES, 0.5 M NaCl, 5% glycerol, 2 mM DTT, pH 7 Temp details: room tempearature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 3, 2018 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→46.225 Å / Num. obs: 16852 / % possible obs: 99.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 51.64 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.161 / Χ2: 0.85 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.6→2.71 Å / Redundancy: 9.6 % / Rmerge(I) obs: 2.404 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1977 / CC1/2: 0.589 / Rpim(I) all: 0.808 / Χ2: 0.56 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.121 Å2
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Refinement step | Cycle: LAST / Resolution: 2.597→46.225 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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