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- PDB-7qi8: 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: 7qi8 | ||||||
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Title | CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR | ||||||
![]() | Lysine--tRNA ligase 1 | ||||||
![]() | LIGASE / Mycobacterium tuberculosis / ATP binding | ||||||
Function / homology | ![]() ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / magnesium ion binding / extracellular space ...ATP:ADP adenylyltransferase activity / lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA binding / magnesium ion binding / extracellular space / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dawson, A. / Robinson, D.A. / Tamjar, J. / Wyatt, P. / Green, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs. Authors: Green, S.R. / Davis, S.H. / Damerow, S. / Engelhart, C.A. / Mathieson, M. / Baragana, B. / Robinson, D.A. / Tamjar, J. / Dawson, A. / Tamaki, F.K. / Buchanan, K.I. / Post, J. / Dowers, K. / ...Authors: Green, S.R. / Davis, S.H. / Damerow, S. / Engelhart, C.A. / Mathieson, M. / Baragana, B. / Robinson, D.A. / Tamjar, J. / Dawson, A. / Tamaki, F.K. / Buchanan, K.I. / Post, J. / Dowers, K. / Shepherd, S.M. / Jansen, C. / Zuccotto, F. / Gilbert, I.H. / Epemolu, O. / Riley, J. / Stojanovski, L. / Osuna-Cabello, M. / Perez-Herran, E. / Rebollo, M.J. / Guijarro Lopez, L. / Casado Castro, P. / Camino, I. / Kim, H.C. / Bean, J.M. / Nahiyaan, N. / Rhee, K.Y. / Wang, Q. / Tan, V.Y. / Boshoff, H.I.M. / Converse, P.J. / Li, S.Y. / Chang, Y.S. / Fotouhi, N. / Upton, A.M. / Nuermberger, E.L. / Schnappinger, D. / Read, K.D. / Encinas, L. / Bates, R.H. / Wyatt, P.G. / 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 | ![]() | 109.4 KB | Display | ![]() |
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PDB format | ![]() | 80.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 788.9 KB | Display | ![]() |
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Full document | ![]() | 798.2 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qh8SC ![]() 7qhnC S: Starting model for refinement 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: 58129.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lysS1, lysS, Rv3598c, MTCY07H7B.24 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-LYS / |
#3: Chemical | ChemComp-DD0 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.42 % / Description: block |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir: 0.25 M NaOAc, 14% PEG 3350 Protein: 100 mM HEPES, 150 mM NaCl, 5% glycerol, pH 7.5, ~ 20 mg/ml Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.33 Å / Num. obs: 27807 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 38.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.092 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.722 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2354 / CC1/2: 0.857 / Rpim(I) all: 0.811 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QH8 Resolution: 2.2→46.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.634 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.01 Å2 / Biso mean: 59.483 Å2 / Biso min: 30.87 Å2
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Refinement step | Cycle: final / Resolution: 2.2→46.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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