Recombinant AcnB, NrdR and RibD of Acinetobacter baumannii and their potential interaction with DNA adenine methyltransferase AamA.

Weber K, Doellinger J, Jeffries CM, Wilharm G, Protein Expr Purif :106134 (2022) Europe PMC

SASDNC5 – Acinetobacter baumannii riboflavin biosynthesis protein RibD

Riboflavin biosynthesis protein RibD
MWexperimental 79 kDa
MWexpected 80 kDa
VPorod 115 nm3
log I(s) 3.34×10-2 3.34×10-3 3.34×10-4 3.34×10-5
Riboflavin biosynthesis protein RibD small angle scattering data  s, nm-1
ln I(s)
Riboflavin biosynthesis protein RibD Guinier plot ln 3.35×10-2 Rg: 3.7 nm 0 (3.7 nm)-2 s2
(sRg)2I(s)/I(0)
Riboflavin biosynthesis protein RibD Kratky plot 1.104 0 √3 sRg
p(r)
Riboflavin biosynthesis protein RibD pair distance distribution function Rg: 3.6 nm 0 Dmax: 12 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Riboflavin biosynthesis protein RibD GASBOR model
log I(s)
 s, nm-1
Riboflavin biosynthesis protein RibD SASREF model
log I(s)
 s, nm-1
Riboflavin biosynthesis protein RibD SREFLEX model
log I(s)
 s, nm-1
Riboflavin biosynthesis protein RibD PDB (PROTEIN DATA BANK) model
Synchrotron SAXS data from solutions of riboflavin biosynthesis protein (RibD) in 150 mM NaCl, 10 mM Tris, 1 mM DTT, 5% v/v glycerol, 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 1.60 mg/ml was measured at 20°C. 20 successive 0.100 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.

Data have been truncated at low-s to remove the effects on the scattering caused by slight non-specific aggregation. From the data displayed in this entry, the concentration independent MW estimates fall in the range of 75–87 kDa. The models displayed in this entry are: Top - a single GASBOR model representative; Second from top - a SASREF refined rigid-body model in P2 symmetry; Third - a SREFLEX normal mode refined model in P1 symmetry (allowing for non-symmetry related movements in the peripheral zinc-binding domain lobes) and; Fourth - the fit to the SAXS data of a closely related Acinetobacter baumannii sp. RibD dimer (PDB, 3ZPG; MW = 77 kDa; UniProt: D0CB74; 97% sequence identity). Additional models and fits, and the full SAXS profile are made available in the full entry zip archive.

Riboflavin biosynthesis protein RibD (RibD)
Mol. type   Protein
Organism   Acinetobacter baumannii
Olig. state   Dimer
Mon. MW   40.1 kDa
 
UniProt   A0A5P1UGY3 (1-361)
Sequence   FASTA
 
PDB ID   3ZPG