Multi-domain structure of a periplasmic chitodextrinase from Vibrio cholerae (VcChdx)

Kanokbhorn Khumnonkhro.

SASDXQ9 – Native state of monomeric full-length glycoside hydrolase family18 chitodextrinase from Vibrio cholerae

Chitodextrinase
MWexperimental 107 kDa
MWexpected 109 kDa
VPorod 125 nm3
log I(s) 1.29×10-1 1.29×10-2 1.29×10-3 1.29×10-4
Chitodextrinase small angle scattering data  s, nm-1
ln I(s)
Chitodextrinase Guinier plot ln 1.29×10-1 Rg: 4.1 nm 0 (4.1 nm)-2 s2
(sRg)2I(s)/I(0)
Chitodextrinase Kratky plot 1.104 0 √3 sRg
p(r)
Chitodextrinase pair distance distribution function Rg: 4.1 nm 0 Dmax: 17.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Native state of monomeric full-length glycoside hydrolase family18 chitodextrinase from Vibrio cholerae Rg histogram Rg, nm
Chitodextrinase EOM/RANCH model
Chitodextrinase EOM/RANCH model
Chitodextrinase EOM/RANCH model
log I(s)
 s, nm-1
Chitodextrinase ALPHAFOLD model
Synchrotron SAXS data from solutions of Native state of monomeric full-length glycoside hydrolase family18 chitodextrinase from Vibrio cholerae in 100mM HEPES, 150mM NaCl, pH 7.5 were collected on the TPS13A beam line at the NSRRC storage ring (Hsinchu, Taiwan) using a Eiger X 1M & 9M detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.0827 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 10°C. 240 successive 2 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 SAS profile obtained by SEC-SAXS connected with Superdex200-increase column size 5x150 mm (Cytiva), flow rate 0.15 mL/min. The 100 µL of 5 mg/mL protein was injected.

Chitodextrinase (ChDex)
Mol. type   Protein
Organism   Vibrio cholerae
Olig. state   Monomer
Mon. MW   108.5 kDa
 
UniProt   Q9KLP3
Sequence   FASTA