Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.

Smith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B, Acta Crystallogr F Struct Biol Commun 74(Pt 1):31-38 (2018) Europe PMC

SASDCH7 – N-terminal domain of DsbD from N. meningitidis

N-terminus of disulfide interchange protein DsbD
MWI(0) 13 kDa
MWexpected 14 kDa
VPorod 17 nm3
log I(s) 7.76×10-3 7.76×10-4 7.76×10-5 7.76×10-6
N-terminus of disulfide interchange protein DsbD small angle scattering data  s, nm-1
ln I(s)
N-terminus of disulfide interchange protein DsbD Guinier plot ln 7.76×10-3 Rg: 1.8 nm 0 (1.8 nm)-2 s2
(sRg)2I(s)/I(0)
N-terminus of disulfide interchange protein DsbD Kratky plot 1.104 0 √3 sRg
p(r)
N-terminus of disulfide interchange protein DsbD pair distance distribution function Rg: 1.7 nm 0 Dmax: 5.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
N-terminus of disulfide interchange protein DsbD DAMMIN model
X-ray synchrotron radiation scattering data from solutions of the n-terminal domain of DsbD from Neisseria meningitidis in 25 mM HEPES 150mM NaCl pH 6.7 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.1127 nm). Thirty successive 2 second frames were collected across solute concentrations of 0.4-5.9 mg/ml. The SAXS data displayed this entry was derived from a 0.74 mg/ml sample as it was deemed to be the highest concentration at which the effects of concentration were negligible. The Rg for n-NmDsbD showed mild concentration dependence above a concentration of 1.0 mg/mL, dropping from ~17.5 Å at 0.4 mg/mL to ~16 Å at 5.9 mg/mL. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN.

N-terminus of disulfide interchange protein DsbD (n-DsbD)
Mol. type   Protein
Organism   Neisseria meningitidis
Olig. state   Monomer
Mon. MW   13.9 kDa
 
UniProt   Q9JTL9 (23-146)
Sequence   FASTA