|Entry||Database: PDB / ID: 4rrq|
|Title||K121M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi with L-Ser3AA|
|Keywords||LIGASE / DTD-like fold / Proofreading|
|Function / homology||Aminoacyl-tRNA synthetase, class II / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-transfer RNA synthetases class-II family profile. / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding ...Aminoacyl-tRNA synthetase, class II / D-aminoacyl-tRNA deacylase-like superfamily / Aminoacyl-transfer RNA synthetases class-II family profile. / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon binding domain / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / Threonine-tRNA ligase, class IIa / Anticodon-binding / Threonine-tRNA ligase catalytic core domain / Threonyl-tRNA synthetase, editing domain, archaea / threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm / Threonine--tRNA ligase|
Function and homology information
|Specimen source||Pyrococcus abyssi GE5 (archaea)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 1.79 Å resolution|
|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
|Date||Deposition: Nov 6, 2014 / Release: Jul 15, 2015|
|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: (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: 2.18 / Density percent sol: 43.69 %|
|Crystal grow||Temp: 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 kelvins|
|Source||Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418|
|Detector||Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Collection date: Jun 15, 2009|
|Radiation||Monochromator: Mirrors / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||D resolution high: 1.79 Å / D resolution low: 25 Å / Number all: 28360 / Number obs: 27566 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Percent possible obs: 97.2|
|Refine||Method to determine structure: MOLECULAR REPLACEMENT / R Free selection details: RANDOM / Sigma F: 2|
|Least-squares process||R factor R free: 0.24 / R factor R work: 0.21 / R factor all: 0.24 / R factor obs: 0.21 / Highest resolution: 1.79 Å / Lowest resolution: 25 Å / Number reflection R free: 1377 / Number reflection all: 28360 / Number reflection obs: 27566|
|Refine hist #LAST||Highest resolution: 1.79 Å / Lowest resolution: 25 Å|
|Number of atoms included #LAST||Protein: 2224 / Nucleic acid: 0 / Ligand: 50 / Solvent: 281 / Total: 2555|
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