Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin

Garcia-Rodriguez G, Girardin Y, Volkov A, Singh R, Muruganandam G, Van Dyck J, Sobott F, Versées W, Charlier D, Loris R, Acta Crystallographica Section D Structural Biology 77(7):904-920 (2021) DOI

SASDKY6 – ParD2 antitoxin from Vibrio cholerae in low salt pH 8

Antitoxin ParD
MWexperimental 109 kDa
MWexpected 108 kDa
VPorod 190 nm3
log I(s) 2.76×10-1 2.76×10-2 2.76×10-3 2.76×10-4
Antitoxin ParD small angle scattering data  s, nm-1
ln I(s)
Antitoxin ParD Guinier plot ln 2.76×10-1 Rg: 3.4 nm 0 (3.4 nm)-2 s2
(sRg)2I(s)/I(0)
Antitoxin ParD Kratky plot 1.104 0 3 sRg
p(r)
Antitoxin ParD pair distance distribution function Rg: 3.3 nm 0 Dmax: 13.9 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of the ParD2 antitoxin from Vibrio cholerae in 20 mM Tris, 150 mM NaCl, 1 mM TCEP, pH 8 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.103219 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 12 mg/ml was injected at a 0.20 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 19°C. The data (0.990 s frames) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Slight repulsive interparticle interference is noted in the Guinier plot and p(r) profile.

Antitoxin ParD
Mol. type   Protein
Organism   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Olig. state   Dodecamer
Mon. MW   9.0 kDa
 
UniProt   P58093 (1-80)
Sequence   FASTA