Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins

Okuda A Inoue R, Kurokawa M, Martel A, Porcar L, Osaki R, Fukuzawa K, Weiss K, Pingali S, Urade R, Sugiyama M, Journal of Applied Crystallography 59(4):1270-1281 (2026) DOI

SASDZS8 – Segmental deuterated Protein disulfide-isomerase A3 comprising three point mutations (D122N/I124L/R363N/Y364G; ER-60 h(a)-pd(bb’)-h(a’))

Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated
MWexperimental 34 kDa
MWexpected 54 kDa
log I(s) 3.13×10-2 3.13×10-3 3.13×10-4 3.13×10-5
Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated small angle scattering data  s, nm-1
ln I(s)
Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated Guinier plot ln 3.14×10-2 Rg: 3.3 nm 0 (3.3 nm)-2 s2
(sRg)2I(s)/I(0)
Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated Kratky plot 1.104 0 3 sRg

Data validation


There are no models related to this curve.

SAXS data from solutions of Segmental deuterated Protein disulfide-isomerase A3 comprising three point mutations (D122N/I124L/R363N/Y364G; ER-60 h(a)-pd(bb’)-h(a’)) in 20 mM Tris-HCl buffer, 150 mM NaCl, 1mM CaCl2, pH 8 were collected on the Rigaku NANOPIX instrument (KURNS, Osaka, Japan) using a HyPix-6000 detector at a sample-detector distance of 1.3 m and at a wavelength of λ = 1.54182 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 4 and 4 mg/ml were measured at 25°C. 72 successive 300 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 low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Two sample-to-detector distance (SDD) conditions, 1330 mm and 300 mm, were used to cover a q range (0.01-0.70 Å-1). Scattering profiles were recorded as 300 s frames, and 72 and 120 frames merged for low q (0.01-0.06 Å-1) and high q (0.06-0.70 Å-1) setups, respectively. We applied the AUC-SAS method to remove aggregation components from the profile.

Protein disulfide-isomerase A3 D122N/I124L/R363N/Y364G segmental deuterated
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   54.1 kDa
 
UniProt   P30101
Sequence   FASTA