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Yorodumi- PDB-5onh: Quaternary complex of wild type E. coli leucyl-tRNA synthetase wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5onh | ||||||
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Title | Quaternary complex of wild type E. coli leucyl-tRNA synthetase with tRNA(leu), leucyl-adenylate analogue, and post-transfer editing analogue of norvaline in the aminoacylation conformation | ||||||
Components |
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Keywords | LIGASE / reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) protein translation / aminoacyl-tRNA activity / leucine-tRNA ligase / class Ia / TRANSLATION | ||||||
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 K-12 (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Palencia, A. / Cusack, S. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. Authors: Dulic, M. / Cvetesic, N. / Zivkovic, I. / Palencia, A. / Cusack, S. / Bertosa, B. / Gruic-Sovulj, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5onh.cif.gz | 443.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5onh.ent.gz | 349.6 KB | Display | PDB format |
PDBx/mmJSON format | 5onh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5onh ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onh | HTTPS FTP |
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-Related structure data
Related structure data | 5omwC 5on2C 5on3C 4aq7S 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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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 K-12 (bacteria) / Gene: leuS, b0642, JW0637 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07813, leucine-tRNA ligase #2: RNA chain | Mass: 28052.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1208670917 |
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-Non-polymers , 4 types, 8 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | |
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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: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 44997 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rsym value: 0.016 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4316 / CC1/2: 0.4 / Rsym value: 1 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4aq7 Resolution: 3.1→222.54 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.592 / SU ML: 0.477 / Cross valid method: THROUGHOUT / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 79.571 Å2
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Refinement step | Cycle: 1 / Resolution: 3.1→222.54 Å
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Refine LS restraints |
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