An Anomalous Small-Angle X-Ray Scattering Study of the Formation of Iron Clusters in the Inner Cavity of the Ferritin-Like Protein Dps

Gordienko A, Mozhaev A, Gibizova V, Dadinova L, Moscow University Physics Bulletin 77(6):858-867 (2023) DOI

SASDPZ7 – DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 2000 iron atoms per dodecamer. Anomalous SAXS spanning the X-ray Fe-absorption edge 7.100-7.133 keV.

DNA protection during starvation protein
MWexperimental 433 kDa
MWexpected 224 kDa
log I(s) 8.50×103 8.50×102 8.50×101 8.50×100
DNA protection during starvation protein small angle scattering data  s, nm-1
ln I(s)
DNA protection during starvation protein Guinier plot ln 8.51×103 Rg: 7.1 nm 0 (7.1 nm)-2 s2
(sRg)2I(s)/I(0)
DNA protection during starvation protein Kratky plot 1.104 0 3 sRg
p(r)
DNA protection during starvation protein pair distance distribution function Rg: 4.2 nm 0 Dmax: 14 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA protection during starvation protein DAMMIN model

log I(s)
 s, nm-1
DNA protection during starvation protein DAMMIN model

log I(s)
 s, nm-1
DNA protection during starvation protein DAMMIN model

Synchrotron SAXS data from solutions of DNA protection during starvation protein (Dps) loaded with FeSO4⋅7H2O in the amount corresponding to 2000 iron atoms per dodecamer in 50 mM NaCl, 0.5 mM EDTA, 50 mM Tris-HCl, pH 8 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.173818 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 10°C. 40 successive 0.095 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The SAXS data in this entry show Dps loaded with FeSO4⋅7H2O in the amount corresponding to 2000 iron atoms per dodecamer measured at 7.133 keV and the corresponding model fits, in addition to the fits to the resonant and non-resonant anomalous SAXS data curves extracted across the Fe X-ray absorption edge (7.100-7.133 keV). The full anomalous SAXS data series, models and fits are made available in the full entry zip archive

DNA protection during starvation protein
Mol. type   Protein
Organism   Escherichia coli (strain K12)
Olig. state   Dodecamer
Mon. MW   18.7 kDa
 
UniProt   P0ABT2 (1-167)
Sequence   FASTA