Medical contrast agents as promising tools for biomacromolecular SAXS experiments.

Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Pérez J, Girard E, Acta Crystallogr D Struct Biol 78(Pt 9):1120-1130 (2022) Europe PMC

SASDNM7 – Protease 1 from Pyrococcus horikoshii (PhP1) in Gd-HPDO3A

Deglycase PH1704
MWexperimental 110 kDa
MWexpected 112 kDa
VPorod 140 nm3
log I(s) 4.18×10-1 4.18×10-2 4.18×10-3 4.18×10-4
Deglycase PH1704 small angle scattering data  s, nm-1
ln I(s)
Deglycase PH1704 Guinier plot ln 4.19×10-1 Rg: 3.2 nm 0 (3.2 nm)-2 s2
(sRg)2I(s)/I(0)
Deglycase PH1704 Kratky plot 1.104 0 √3 sRg
Dmax: 9.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Deglycase PH1704 OTHER model
Synchrotron SAXS data from solutions of Protease 1 from Pyrococcus horikoshii (PhP1) in 20 mM Tris pH 7.5, 150 mM NaCl, were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 8.40 mg/ml was measured at 15°C. 10 successive 1 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 data displayed in this entry is that of hexameric Protease 1 without the addition of gadoteridol, Gd-HPDO3A, that acts as X-ray contrast variation agent. Refer to the full entry zip archive that contains additional SAXS data and model fits in the presence of 0-1016 mM Gd-HPDO3A (https://pubchem.ncbi.nlm.nih.gov/compound/Gadoteridol).

Deglycase PH1704
Mol. type   Protein
Organism   Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Olig. state   Hexamer
Mon. MW   18.6 kDa
 
UniProt   O59413 (1-166)
Sequence   FASTA