Structural basis for control of integrative and conjugative element excision and transfer by the oligomeric winged helix–turn–helix protein RdfS

Verdonk C, Agostino M, Eto K, Hall D, Bond C, Ramsay J, Nucleic Acids Research 53(6) (2025) DOI

SASDW97 – Recombination directionality factor (6H-RdfS) from M.japonicum bound to 40mer DNA

Recombination directionality factor RdfS
attP_8 40-mer DNA
MWexperimental 83 kDa
MWexpected 77 kDa
VPorod 134 nm3
log I(s) 8.53×10-2 8.53×10-3 8.53×10-4 8.53×10-5
Recombination directionality factor RdfS attP_8 40-mer DNA small angle scattering data  s, nm-1
ln I(s)
Recombination directionality factor RdfS attP_8 40-mer DNA Guinier plot ln 8.54×10-2 Rg: 3.8 nm 0 (3.8 nm)-2 s2
(sRg)2I(s)/I(0)
Recombination directionality factor RdfS attP_8 40-mer DNA Kratky plot 1.104 0 √3 sRg
p(r)
Recombination directionality factor RdfS attP_8 40-mer DNA pair distance distribution function Rg: 3.8 nm 0 Dmax: 13.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Recombination directionality factor RdfS attP_8 40-mer DNA OTHER model
log I(s)
 s, nm-1
Recombination directionality factor RdfS attP_8 40-mer DNA DAMMIF model
Synchrotron SAXS data from solutions of His-tagged RdfS excisionase bound to dsDNA 40mer attP_8 in 150 mM Tris-HCl, 300 mM NaCl, 5% v/v glycerol, pH 7.4 were collected on the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.6 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 50.00 μl samples at 6H-RdfS at 390 µM, dsDNA attP_8 at 500 µM was injected at a 0.30 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 23°C. 36 successive 1 second data frames were selected from the SEC sample peak (from a total of 800 individual frames measured from the entire SEC elution) and processed to generate the profile displayed in this entry. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Recombination directionality factor RdfS (RdfS)
Mol. type   Protein
Organism   Mesorhizobium japonicum R7A
Olig. state   Tetramer
Mon. MW   12.9 kDa
 
UniProt   Q7AL96
Sequence   FASTA
 
attP_8 40-mer DNA (attP_8)
Mol. type   DNA
Olig. state   Dimer
Mon. MW   12.6 kDa
Sequence   FASTA