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 Feb 27)

doi: 10.1107/S2059798323001249

Submitted to SASBDB: 2022 Dec 23 Published in SASBDB: 2023 Mar 8

SASDQB9 – YdaT_toxin domain-containing protein Sample: YdaT_toxin domain-containing protein tetramer, 74 kDa Escherichia coli O157:H7 protein Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8 Experiment: SAXS data collected at SWING, SOLEIL on 2022 Apr 16 RgGuinier 3.5 nm Dmax 12.0 nm VolumePorod 130 nm3

SASDQC9 – Mutant YdaT_toxin domain-containing protein (L111N/F118R) Sample: YdaT_toxin domain-containing protein (mutant: L111N, F118R) monomer, 18 kDa Escherichia coli O157:H7 protein Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8 Experiment: SAXS data collected at SWING, SOLEIL on 2021 Apr 14 RgGuinier 2.4 nm Dmax 8.2 nm VolumePorod 32 nm3

SASDQD9 – N-terminal domain of YdaT_toxin domain-containing protein Sample: YdaT_toxin domain-containing protein monomer, 13 kDa Escherichia coli O157:H7 protein Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8 Experiment: SAXS data collected at SWING, SOLEIL on 2022 Apr 16 RgGuinier 1.7 nm Dmax 5.7 nm VolumePorod 29 nm3

SASDQE9 – YdaT_toxin domain-containing protein bound to 30 base pair dsDNA Sample: YdaT_toxin domain-containing protein tetramer, 74 kDa Escherichia coli O157:H7 protein Om 30 base pair dsDNA dimer, 37 kDa DNA Buffer: 20 mM Tris-HCl, 200 mM NaCl, pH: 8 Experiment: SAXS data collected at BM29, ESRF on 2021 Apr 14 RgGuinier 4.2 nm Dmax 12.8 nm VolumePorod 190 nm3