Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7

Prolič-Kalinšek M, Volkov A, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R, Acta Crystallographica Section D Structural Biology 79(3):245-258 (2023) DOI

SASDQD9 – N-terminal domain of YdaT_toxin domain-containing protein

YdaT_toxin domain-containing protein
MWexperimental 11 kDa
MWexpected 13 kDa
VPorod 29 nm3
log I(s) 1.06×10-2 1.06×10-3 1.06×10-4 1.06×10-5
YdaT_toxin domain-containing protein small angle scattering data  s, nm-1
ln I(s)
YdaT_toxin domain-containing protein Guinier plot ln 1.06×10-2 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
YdaT_toxin domain-containing protein Kratky plot 1.104 0 √3 sRg
p(r)
YdaT_toxin domain-containing protein pair distance distribution function Rg: 1.8 nm 0 Dmax: 5.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
YdaT_toxin domain-containing protein OTHER [STATIC IMAGE] model
Synchrotron SAXS data from solutions of the N-terminal domain of YdaT_toxin domain-containing protein in 20 mM Tris-HCl, 200 mM NaCl, 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 2.2 m and at a wavelength of λ = 0.103 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 45.00 μl sample at 10 mg/ml was injected at a 0.30 ml/min flow rate onto a Shodex KW402.5-4F column at 15°C. 630 successive 0.990 second frames were collected through the SEC elution. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The atomic coordinate file of the full ensemble is made available in the full entry zip archive.

YdaT_toxin domain-containing protein (YdaT)
Mol. type   Protein
Organism   Escherichia coli O157:H7
Olig. state   Monomer
Mon. MW   13.3 kDa
 
UniProt   A0A6M7H0F8 (2-96)
Sequence   FASTA