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Yorodumi- PDB-5ags: Crystal structure of the LeuRS editing domain of Mycobacterium tu... -
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-Basic information
Entry | Database: PDB / ID: 5ags | ||||||
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Title | Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct 3-(Aminomethyl)-4-bromo-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP | ||||||
Components | LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / M.TUBERCULOSIS / LEUCINE-TRNA LIGASE ACTIVITY / ATP + L-LEUCINE + TRNA(LEU) GIVES AMP + DIPHOSPHATE + L-LEUCYL- TRNA(LEU) AMINOACYL-TRNA EDITING ACTIVITY / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / NOVEL BORON INHIBITORS OF LEURS | ||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Palencia, A. / Li, X. / Alley, M.R.K. / Ding, C. / Easom, E.E. / Hernandez, V. / Meewan, M. / Mohan, M. / Rock, F.L. / Franzblau, S.G. ...Palencia, A. / Li, X. / Alley, M.R.K. / Ding, C. / Easom, E.E. / Hernandez, V. / Meewan, M. / Mohan, M. / Rock, F.L. / Franzblau, S.G. / Wang, Y. / Lenaerts, A.J. / Parish, T. / Cooper, C.B. / Waters, M.G. / Ma, Z. / Mendoza, A. / Barros, D. / Cusack, S. / Plattner, J.J. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2016 Title: Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium Tuberculosis that Target Leucyl-tRNA Synthetase. Authors: Palencia, A. / Li, X. / Bu, W. / Choi, W. / Ding, C.Z. / Easom, E.E. / Feng, L. / Hernandez, V. / Houston, P. / Liu, L. / Meewan, M. / Mohan, M. / Rock, F.L. / Sexton, H. / Zhang, S. / Zhou, ...Authors: Palencia, A. / Li, X. / Bu, W. / Choi, W. / Ding, C.Z. / Easom, E.E. / Feng, L. / Hernandez, V. / Houston, P. / Liu, L. / Meewan, M. / Mohan, M. / Rock, F.L. / Sexton, H. / Zhang, S. / Zhou, Y. / Wan, B. / Wang, Y. / Franzblau, S.G. / Woolhiser, L. / Gruppo, V. / Lenaerts, A.J. / O'Malley, T. / Parish, T. / Cooper, C.B. / Waters, M.G. / Ma, Z. / Ioerger, T.R. / Sacchettini, J.C. / Rullas, J. / Angulo-Barturen, I. / Perez-Herran, E. / Mendoza, A. / Barros, D. / Cusack, S. / Plattner, J.J. / Alley, M.R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ags.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ags.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ags.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5ags ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5ags | HTTPS FTP |
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-Related structure data
Related structure data | 5agrC 5agtC 2ajgS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 24890.756 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1, RESIDUES 309-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DE3 RIL / References: UniProt: P9WFV1, leucine-tRNA ligase |
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#2: Chemical | ChemComp-MET / |
#3: Chemical | ChemComp-38Y / |
#4: Water | ChemComp-HOH / |
Sequence details | CONTAINS A N-TERM SEQUENCE BELONGING TO PETM-11 EMBL VECTOR |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.9 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1 M BIS-TRIS PH 5.5, 17% W/V PEG 10000, 0.2 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→38.7 Å / Num. obs: 35180 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.47→1.51 Å / Redundancy: 4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AJG Resolution: 1.47→38.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.133 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.287 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→38.69 Å
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Refine LS restraints |
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