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- PDB-5ah5: Crystal structure of the ternary complex of Agrobacterium radioba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ah5 | ||||||
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Title | Crystal structure of the ternary complex of Agrobacterium radiobacter K84 agnB2 LeuRS-tRNA-LeuAMS | ||||||
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![]() | LIGASE/RNA / LIGASE-RNA COMPLEX / LEUCINE-TRNA / LEUCINE-TRNA LIGASE ACTIVITY ATP + L-LEUCINE + TRNA(LEU) GIVES AMP + DIPHOSPHATE + L-LEUCYL-TRNA(LEU) / AMINOACYL- TRNA EDITING ACTIVITY / AMINOACYL-TRNA SYNTHETASE / PROTEIN BIOSYNTHESIS / TOXIC MOEITY 84 RESISTANCE | ||||||
Function / homology | ![]() leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palencia, A. / Chopra, S. / Virus, C. / Schulwitz, S. / Temple, B.R. / Cusack, S. / Reader, J.S. | ||||||
![]() | ![]() Title: Structural Characterization of Antibiotic Self-Immunity tRNA Synthetase in Plant Tumour Biocontrol Agent. Authors: Chopra, S. / Palencia, A. / Virus, C. / Schulwitz, S. / Temple, B.R. / Cusack, S. / Reader, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 427.7 KB | Display | ![]() |
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PDB format | ![]() | 341.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 68.4 KB | Display | |
Data in CIF | ![]() | 102.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 ABCD
#1: Protein | Mass: 92351.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: RNA chain | Mass: 26959.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 882 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/LSS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LSS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | CONTAINS A C-TERM TAG BELONGING TO THE EXPRESSION |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58.5 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 27 % PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.6 Å / Num. obs: 160330 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2BTE, 4AS1 Resolution: 2.1→48.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.191 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / 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: 50.507 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→48.58 Å
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Refine LS restraints |
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