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Yorodumi- PDB-3zgz: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zgz | ||||||
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Title | Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and toxic moiety from agrocin 84 (TM84) in aminoacylation-like conformation | ||||||
Components |
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Keywords | LIGASE/RNA / LIGASE-RNA COMPLEX / LIGASE / NUCLEOTIDE(ATP)-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA 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: 2.4 Å | ||||||
Authors | Chopra, S. / Palencia, A. / Virus, C. / Tripathy, A. / Temple, B.R. / Velazquez-Campoy, A. / Cusack, S. / Reader, J.S. | ||||||
Citation | Journal: Nat.Commun. / Year: 2013 Title: Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase Authors: Chopra, S. / Palencia, A. / Virus, C. / Tripathy, A. / Temple, B.R. / Velazquez-Campoy, A. / Cusack, S. / Reader, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zgz.cif.gz | 881.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zgz.ent.gz | 720.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/3zgz ftp://data.pdbj.org/pub/pdb/validation_reports/zg/3zgz | HTTPS FTP |
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-Related structure data
Related structure data | 4aq7S 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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2 |
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Unit cell |
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-Components
-Protein / RNA chain , 2 types, 4 molecules ADBE
#1: Protein | Mass: 99516.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07813, leucine-tRNA ligase #2: RNA chain | Mass: 28396.875 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI K-12 (bacteria) |
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-Non-polymers , 4 types, 380 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | TOXIC MOIETY FROM AGROCIN 84 (TM84) (84T): TM84 WAS PURIFIED FROM CELLULAR CULTURES OF ...TOXIC MOIETY FROM AGROCIN 84 (TM84) (84T): TM84 WAS PURIFIED FROM CELLULAR CULTURES OF AGROBACTER |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.1 M BIS-TRIS, 23-25 % PEG 3350, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 85255 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 65.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AQ7 Resolution: 2.4→43.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.952 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 48.815 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.59 Å
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Refine LS restraints |
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