Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD).

Yaacob N, Kamonsutthipaijit N, Soontaranon S, Leow TC, Rahman RNZRA, Ali MSM, Int J Biol Macromol (2022) Europe PMC

SASDEX6 – Cold-active AMS8 lipase in the presence of calcium (without polyhistidine affinity tag)

LipAMS8
MWI(0) 40 kDa
MWexpected 50 kDa
VPorod 87 nm3
log I(s) 7.77×101 7.77×100 7.77×10-1 7.77×10-2
LipAMS8 small angle scattering data  s, nm-1
ln I(s)
LipAMS8 Guinier plot ln 7.77×101 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
LipAMS8 Kratky plot 1.104 0 √3 sRg
p(r)
LipAMS8 pair distance distribution function Rg: 3.0 nm 0 Dmax: 9.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
LipAMS8 DAMMIF model
Synchrotron SAXS data from solutions of cold-active AMS8 lipase (without polyhistidine affinity tag) in 50 mM Tris HCl, 5 mM CaCl2, pH 8 were collected on the BL1.3W SAXS/WAXS beam line at the Synchrotron Light Research Institute (SLRI; Nakhon Ratchasima, Thailand) using a MAR 345 Image Plate detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.138 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 25°C. One 600 second frame was collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

LipAMS8 (AMS8)
Mol. type   Protein
Organism   Pseudomonas sp. AMS8
Olig. state   Monomer
Mon. MW   50.0 kDa
 
UniProt   E1B2U7 (1-476)
Sequence   FASTA