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Yorodumi- PDB-3zjv: Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and ... -
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-Basic information
Entry | Database: PDB / ID: 3zjv | ||||||
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Title | Ternary complex of E .coli leucyl-tRNA synthetase, tRNA(Leu) and the benzoxaborole AN3213 in the editing conformation | ||||||
Components |
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Keywords | LIGASE/RNA / LIGASE-RNA COMPLEX / LIGASE / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE / AMINOACYL TRNA SYNTHETASE / ATP BINDING / EDITING SYNTHETASE | ||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Cusack, S. / Palencia, A. / Crepin, T. / Hernandez, V. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. ...Cusack, S. / Palencia, A. / Crepin, T. / Hernandez, V. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / Sheoran, A. / Zhang, Y. / Zhang, Y. / Zhou, Y. / Nieman, J.A. / Anugula, M.R. / Keramane, E.M. / Savariraj, K. / Reddy, D.S. / Sharma, R. / Subedi, R. / Singh, R. / OLeary, A. / Simon, N.L. / DeMarsh, P.L. / Mushtaq, S. / Warner, M. / Livermore, D.M. / Alley, M.R.K. / Plattner, J.J. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 Title: Discovery of a Novel Class of Boron-Based Antibacterials with Activity Against Gram-Negative Bacteria. Authors: Hernandez, V. / Crepin, T. / Palencia, A. / Cusack, S. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / ...Authors: Hernandez, V. / Crepin, T. / Palencia, A. / Cusack, S. / Akama, T. / Baker, S.J. / Bu, W. / Feng, L. / Freund, Y.R. / Liu, L. / Meewan, M. / Mohan, M. / Mao, W. / Rock, F.L. / Sexton, H. / Sheoran, A. / Zhang, Y. / Zhang, Y. / Zhou, Y. / Nieman, J.A. / Anugula, M.R. / Keramane, E.M. / Savariraj, K. / Reddy, D.S. / Sharma, R. / Subedi, R. / Singh, R. / O'Leary, A. / Simon, N.L. / De Marsh, P.L. / Mushtaq, S. / Warner, M. / Livermore, D.M. / Alley, M.R.K. / Plattner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zjv.cif.gz | 422.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zjv.ent.gz | 338 KB | Display | PDB format |
PDBx/mmJSON format | 3zjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zjv_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 3zjv_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 3zjv_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 3zjv_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/3zjv ftp://data.pdbj.org/pub/pdb/validation_reports/zj/3zjv | HTTPS FTP |
-Related structure data
Related structure data | 3zjtC 3zjuC 1h3nS 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: 99516.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase |
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#2: RNA chain | Mass: 28270.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNMODIFIED T7 TRANSCRIPT / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN3213 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE AT PH 5.6, 14-18 % PEG 6000 AND 200 MM NACL. CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING A CRYOPROTECTING ...Details: THE TERNARY COMPLEX ECLEURS-TRNA-AN3213 WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE AT PH 5.6, 14-18 % PEG 6000 AND 200 MM NACL. CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING A CRYOPROTECTING SOLUTION CONTAINING 22 % ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→88.7 Å / Num. obs: 52864 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.31→2.37 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H3N Resolution: 2.31→88.74 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.808 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES RESIDUAL ONLY
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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 mean: 38.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→88.74 Å
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Refine LS restraints |
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