X-ray structure of wheat germ agglutinin isolectin 3

Wheat germ agglutinin isolectin 3 (WGA3) was crystallized from 10 mM acetate buffer at pH 4.9 containing 6 mM CaCl₂ and 4%(v/v) ethanol. The crystal belongs to monoclinic space group P2₁ with unit-cell dimensions a = 44.86, b = 91.02, c = 44.86 Å, and β = 110.22°. The asymmetric unit contains two molecules (V_m = 2.51 ų Da⁻¹). The crystal structure was solved by the molecular-replacement method and was refined by the simulated-annealing method. The conventional R value was 0.191 for 19713 reflections [F_o > 3σ(F)] in the resolution range 8–1.9 Å. The r.m.s. deviations from the ideal bond distances and angles were 0.014 Å, and 3.0°, respectively, and the estimated coordinate error was 0.2–0.25 Å. The two molecules in the asymmetric unit are related by the pseudo twofold symmetry and form a dimer structure. The backbone structures of the two subunits are nearly identical with the r.m.s. difference of 0.36 Å for the superposition of equivalent C^α atoms. The dimer structure is very similar to those of isolectins 1 and 2 with the r.m.s. difference of 0.35–0.39 Å for the C^α superposition. Since amino-acid residues which differ from those of isolectin 1 or 2 are not involved in the contact between the two subunits, the subunit–subunit interaction is not significantly affected by the replacement of these residues. As a result, the geometry of the sugar-binding sites which are located at the interface between the two subunit molecules is basically conserved among three isolectins.