Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model?

Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P, Biochemical and Biophysical Research Communications :152677 (2025) DOI

SASDX48 – SmThrRS model based on PDB entries 6vu9 and 1qf6

Stenotrophomonas maltophilia threonyl tRNA synthetase
MWexperimental 141 kDa
MWexpected 146 kDa
log I(s) 6.43×101 6.43×100 6.43×10-1 6.43×10-2
Stenotrophomonas maltophilia threonyl tRNA synthetase small angle scattering data  s, nm-1
ln I(s)
Stenotrophomonas maltophilia threonyl tRNA synthetase Guinier plot ln 6.44×101 Rg: 4.2 nm 0 (4.2 nm)-2 s2
(sRg)2I(s)/I(0)
Stenotrophomonas maltophilia threonyl tRNA synthetase Kratky plot 1.104 0 3 sRg
p(r)
Stenotrophomonas maltophilia threonyl tRNA synthetase pair distance distribution function 0 r

Data validation


Fits and models


log I(s)
 s, nm-1
Stenotrophomonas maltophilia threonyl tRNA synthetase PDB (PROTEIN DATA BANK) model

log I(s)
 s, nm-1

Synchrotron SAXS data from solutions of SmThrRS model based on PDB entries 6vu9 and 1qf6 in 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.10 mg/ml was measured at 20°C. 660 successive 2 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The trace was processed with Chromixs. The IFT was computed in BioXtas-RAW 2.3.0. The Dmax was set to 162 Angstroms. GNOM gives a similar Dmax at a qmax of 0.3 A^-1.

Stenotrophomonas maltophilia threonyl tRNA synthetase (SmThrRS)
Mol. type   Protein
Olig. state   Dimer
Mon. MW   72.9 kDa
 
UniProt   B2FN79
Sequence   FASTA
 
PDB ID   6VU9