Refined structure of basic phospholipase A2 from venom of Agkistrodon halys Pallas in orthorhombic crystal form I at 0.25 nm resolution

The basic phospholipase A2 from the venom ofAgkistrodon halys Pallas is a potent hemolytic toxin and anticoagulant. The accurate rotation and translation parameters of the molecules in orthorhombic crystal form I were successfully obtained using the fitting refinement technique. The structure was refined in the resolution range of 0.6–0.25 nm using least square refinement with non-crystallographic two fold symmetry restraint, and resulted in the finalR factor of 20.1 %, and the rms deviations from ideal stereochemistry were 0.001 3 nm for bond lengths and 1.32° for bond angles. The overall architecture of the present structure was similar to that of the determined structure of the orthorhombic crystal form II, with a few differences in the regions of the β-wing and Ca²⁺ -binding Imp. The dimers formed by the two molecules in the asymmetric unit in both crystal forms were also similar. However, one of the monomers showed an orientational difference of 5.5° along the dimer interface in the two crystal forms, suggesting the flexibility of the interface of the dimer to some degree. The molecular packing of the dimer in crystal form I was much more compact than that in crystal form II. Project supported by the Chinese Academy of Sciences.