High-accuracy protein structure modeling and its application to molecular replacement of crystallographic phasing

We have solved the crystal structures of predicted fructose-specific enzyme IIBfruc from Escherichia coli (EcEIIBfruc) and D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB) of which the X-ray data contain various crystallographic problems. The bottleneck of the structural determination by X-ray crystallography was the phasing of the diffraction data. The obstacles were overcome by molecular replacement (MR) using the GOT(Global-Optimization-based Template-based modeling of proteins) models combined with the exhaustive search by bruteforce automation of phasing trials. This study suggests that the current computational approach can be applied to many unsolved MR problems where better 3D protein models are required or/and the MR solution is limited by the ambiguity in the crystallographic data.