|Entry||Database: PDB / ID: 4rrr|
|Title||K121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Thr3AA|
|Keywords||LIGASE / DTD-like fold / Proofreading|
|Function / homology|
Function and homology information
threonine-tRNA ligase / threonine-tRNA ligase activity / threonyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Aminoacyl-tRNA synthetase, class II / Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon-binding domain superfamily / Threonine-tRNA ligase catalytic core domain / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding / D-tyrosyl-tRNA(Tyr) deacylase ...Aminoacyl-tRNA synthetase, class II / Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon-binding domain superfamily / Threonine-tRNA ligase catalytic core domain / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding / D-tyrosyl-tRNA(Tyr) deacylase / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
|Biological species||Pyrococcus abyssi GE5 (archaea)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å|
|Authors||Hussain, T. / Kamarthapu, V. / Sankaranarayanan, R.|
|Citation||Journal: Nat Commun / Year: 2015|
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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: Threonine--tRNA ligase
B: Threonine--tRNA ligase
Mass: 16740.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-147 / Mutation: K121M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: thrS, PYRAB13430, PAB1490 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UZ14, threonine-tRNA ligase
|#2: Chemical||#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 1.84 Å3/Da / Density % sol: 33.16 %|
|Crystal grow||Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 |
Details: BisTris, NaCl, PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å|
|Detector||Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 22, 2009|
|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: 1.86→25 Å / Num. all: 20823 / Num. obs: 20636 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→25 Å|
|Refinement step||Cycle: LAST / Resolution: 1.86→25 Å|
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