Integrative Structural Characterization of Candida glabrata Phosphoglycerate Kinase by Small-Angle X-ray Scattering and AlphaFold: Implications for Therapeutic Targeting in Candidiasis

Cuéllar-Cruz M, Maqueda Cabrera E, Siliqi D, Moreno A, ACS Omega (2026) DOI

SASDXB2 – Phosphoglycerate kinase

Phosphoglycerate kinase
MWexperimental 47 kDa
MWexpected 45 kDa
VPorod 79 nm3
log I(s) 5.48×10-2 5.48×10-3 5.48×10-4 5.48×10-5
Phosphoglycerate kinase small angle scattering data  s, nm-1
ln I(s)
Phosphoglycerate kinase Guinier plot ln 5.49×10-2 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
Phosphoglycerate kinase Kratky plot 1.104 0 √3 sRg
p(r)
Phosphoglycerate kinase pair distance distribution function Rg: 2.9 nm 0 Dmax: 10.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Phosphoglycerate kinase ALPHAFOLD model
log I(s)
 s, nm-1
Phosphoglycerate kinase GASBOR model
Synchrotron SAXS data from solutions of Phosphoglycerate kinase enzyme in 50 mM sodium phosphate, 500 mM NaCl, 500 mM imidazole, and 1 mM phenylmethylsulfonyl fluoride (PMSF) at pH 8.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 6 mg/ml was injected at a 0.07 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 15°C. 620 successive 3 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.

Phosphoglycerate kinase (PgK)
Mol. type   Protein
Organism   Nakaseomyces glabratus
Olig. state   Monomer
Mon. MW   44.6 kDa
 
UniProt   A0A0W0EGC5 (1-416)
Sequence   FASTA