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Yorodumi- PDB-2v0c: LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A... -
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-Basic information
Entry | Database: PDB / ID: 2v0c | ||||||
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Title | LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site | ||||||
Components | AMINOACYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / CLSS I AMINOACYL- TRNA SYNTHETASE / ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI + L-LEUCYL-TRNA(LEU) / AMINOACYL-TRNA SYNTHETASE / ZINC / ATP-BINDING / METAL-BINDING | ||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | THERMUS THERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. ...Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K. | ||||||
Citation | Journal: Science / Year: 2007 Title: An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site. Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / ...Authors: Rock, F. / Mao, W. / Yaremchuk, A. / Tukalo, M. / Crepin, T. / Zhou, H. / Zhang, Y. / Hernandez, V. / Akama, T. / Baker, S. / Plattner, J. / Shapiro, L. / Martinis, S.A. / Benkovic, S.J. / Cusack, S. / Alley, M.R.K. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v0c.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v0c.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 2v0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/2v0c ftp://data.pdbj.org/pub/pdb/validation_reports/v0/2v0c | HTTPS FTP |
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-Related structure data
Related structure data | 2v0gC 1h3nS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 100997.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB-27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIE4 |
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-Non-polymers , 6 types, 694 molecules
#2: Chemical | ChemComp-LEU / | ||||||
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#3: Chemical | ChemComp-LMS / [( | ||||||
#4: Chemical | #5: Chemical | ChemComp-ANZ / [( | #6: Chemical | ChemComp-SO4 / #7: 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: 3.5 Å3/Da / Density % sol: 64.4 % |
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Crystal grow | Details: PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 472672 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.86 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.42 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H3N Resolution: 1.85→87.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.236 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. C-TERMINAL DOMAIN RESIDUES 814-878 ARE DISORDERED
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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: 21.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→87.37 Å
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Refine LS restraints |
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