Protein quaternary structures in solution are a mixture of multiple forms

Marciano S, Dey D, Listov D, Fleishman S, Sonn-Segev A, Mertens H, Busch F, Kim Y, Harvey S, Wysocki V, Schreiber G, Chemical Science 13(39):11680-11695 (2022) DOI

SASDLP4 – Superoxide dismutase, SodA

Superoxide dismutase [Mn]
MWI(0) 46 kDa
MWexpected 23 kDa
VPorod 54 nm3
log I(s) 3.41×10-2 3.41×10-3 3.41×10-4 3.41×10-5
Superoxide dismutase [Mn] small angle scattering data  s, nm-1
ln I(s)
Superoxide dismutase [Mn] Guinier plot ln 3.42×10-2 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
Superoxide dismutase [Mn] Kratky plot 1.104 0 √3 sRg
p(r)
Superoxide dismutase [Mn] pair distance distribution function Rg: 2.3 nm 0 Dmax: 7.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Superoxide dismutase [Mn] PDB (PROTEIN DATA BANK) model
Superoxide dismutase [Mn] PDB (PROTEIN DATA BANK) model
Superoxide dismutase [Mn] PDB (PROTEIN DATA BANK) model
log I(s)
 s, nm-1
Superoxide dismutase [Mn] OTHER model
Synchrotron SAXS data from solutions of Superoxide dismutase, SodA. in 50 mM HEPES, pH 7.4 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 = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.03 mg/ml was measured at 20°C. 40 successive 0.050 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.

Models. Top: An oligomer fit to the data (volume fraction weighted fit of monomers, dimers and tetramers). Bottom: Dimer only fit to the data.

Superoxide dismutase [Mn] (SodA)
Mol. type   Protein
Organism   Escherichia coli (strain K12)
Olig. state   Unknown
Mon. MW   23 kDa
 
UniProt   P00448 (1-206)
Sequence   FASTA
 
PDB ID   1D5N
 
PDB ID   1D5N
 
PDB ID   1D5N