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- PDB-4rrg: Editing domain of threonyl-tRNA synthetase from Methanococcus jan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rrg | ||||||
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Title | Editing domain of threonyl-tRNA synthetase from Methanococcus jannaschii with L-Thr3AA | ||||||
![]() | Threonine--tRNA ligase | ||||||
![]() | LIGASE / DTD-like fold / Proofreading | ||||||
Function / homology | ![]() threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ahmad, S. / Yerabham, A.S.K. / Kamarthapu, V. / Sankaranarayanan, R. | ||||||
![]() | ![]() Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.6 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rr6C ![]() 4rr7C ![]() 4rr8C ![]() 4rr9C ![]() 4rraC ![]() 4rrbC ![]() 4rrcC ![]() 4rrdC ![]() 4rrfC ![]() 4rrhC ![]() 4rriC ![]() 4rrjC ![]() 4rrkC ![]() 4rrlC ![]() 4rrmC ![]() 4rrqC ![]() 4rrrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15951.302 Da / Num. of mol.: 4 / Fragment: UNP residues 1-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: thrS, MJ1197 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris HCl, 0.2M MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2011 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→25 Å / Num. all: 32970 / Num. obs: 32739 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 28.864 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→24.55 Å
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Refine LS restraints |
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