Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans.

Kryl M, Sedláček V, Kučera I, Int J Mol Sci 24(4) (2023) Europe PMC

SASDD73 – Flavin reductase Pden_5119

NADPH-dependent FMN reductase
MWexperimental 41 kDa
MWexpected 41 kDa
VPorod 70 nm3
log I(s) 1.40×10-1 1.40×10-2 1.40×10-3 1.40×10-4
NADPH-dependent FMN reductase small angle scattering data  s, nm-1
ln I(s)
NADPH-dependent FMN reductase Guinier plot ln 1.40×10-1 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
NADPH-dependent FMN reductase Kratky plot 1.104 0 3 sRg
p(r)
NADPH-dependent FMN reductase pair distance distribution function Rg: 2.3 nm 0 Dmax: 6.3 nm

Data validation


Fits and models


log I(s)
 s, nm-1
NADPH-dependent FMN reductase SWISSMODEL model

log I(s)
 s, nm-1
NADPH-dependent FMN reductase DAMMIN model

SAXS data from solutions of flavin reductase Pden_5119 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8, were collected on a Rigaku BioSAXS-1000 instrument at the Central European Institute of Technology, CEITEC, (Brno, Czech Republic) using a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.5 and 7.5 mg/ml were measured at 4°C. 30 successive 600 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 low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

NADPH-dependent FMN reductase (Pden_5119)
Mol. type   Protein
Organism   Paracoccus denitrificans
Olig. state   Dimer
Mon. MW   20.6 kDa
 
UniProt   A1BCD5
Sequence   FASTA
 
PDB ID   4C76