Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element

Verdonk C, Marshall A, Ramsay J, Bond C, Acta Crystallographica Section D Structural Biology 78(10) (2022) DOI

SASDPK4 – His-tagged RdfS Excisionase monomeric in solution

DNA-binding protein
MWI(0) 12 kDa
MWexpected 13 kDa
VPorod 23 nm3
log I(s) 1.05×10-2 1.05×10-3 1.05×10-4 1.05×10-5
DNA-binding protein small angle scattering data  s, nm-1
ln I(s)
DNA-binding protein Guinier plot ln 1.05×10-2 Rg: 2.2 nm 0 (2.2 nm)-2 s2
DNA-binding protein Kratky plot 1.104 0 3 sRg
DNA-binding protein pair distance distribution function Rg: 2.4 nm 0 Dmax: 9.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
His-tagged RdfS Excisionase monomeric in solution Rg histogram Rg, nm
DNA-binding protein EOM/RANCH model
DNA-binding protein OTHER [STATIC IMAGE] model

log I(s)
 s, nm-1
DNA-binding protein DAMMIF model

Synchrotron SAXS data from solutions of His-tagged RdfS excisionase 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 sample at 6.8 mg/ml was injected at a 0.30 ml/min flow rate onto a GE Superdex 200 Increase 5/150 column at 23°C. 18 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.

The complete results from ensemble optimisation method (EOM), as well as DAMMIF/DAMAVER and CORAL rigid-body modelling are included in the full entry zip archive.

DNA-binding protein
Mol. type   Protein
Organism   Mesorhizobium loti
Olig. state   Monomer
Mon. MW   12.9 kDa
UniProt   Q7AL96
Sequence   FASTA