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- PDB-4arc: Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4arc | ||||||
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Title | Ternary complex of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucine in the editing conformation | ||||||
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![]() | LIGASE/RNA / LIGASE-RNA COMPLEX / NUCLEOTIDE-BINDING / PROTEIN BIOSYNTHESIS / CLASS I AMINOACYL-TRNA SYNTHETASE / ATP-BINDING / METAL-BINDING | ||||||
Function / homology | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S. | ||||||
![]() | ![]() Title: Structural Dynamics of the Aminoacylation and Proofreading Functional Cycle of Bacterial Leucyl-tRNA Synthetase Authors: Palencia, A. / Crepin, T. / Vu, M.T. / Lincecum Jr, T.L. / Martinis, S.A. / Cusack, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.5 KB | Display | ![]() |
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PDB format | ![]() | 172.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.4 KB | Display | ![]() |
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Full document | ![]() | 494.8 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aq7C ![]() 4ariC ![]() 4as1C ![]() 1h3nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 28052.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNMODIFIED T7 TRANSCRIPT / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-LEU / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: THE TERNARY COMPLEX ECLEURS-TRNA-LEU WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 200 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ...Details: THE TERNARY COMPLEX ECLEURS-TRNA-LEU WAS CRYSTALLIZED FROM 0.1 M SODIUM ACETATE (PH 5.6), 14-18% (W/V) PEG 6000 AND 200 MM NACL. THE CRYSTALS WERE FROZEN IN LIQUID NITROGEN USING 22% (V/V) ETHYLENE GLYCOL AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07225 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 87917 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H3N Resolution: 2→45.57 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.325 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.166 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.403 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.57 Å
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Refine LS restraints |
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