Structure of rabbit muscle phosphoglucomutase refined at 2.4 angstrom resolution

Data between 6.0 and 2.4 Angstrom resolution, collected at 253 K, were used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (R-free = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 Angstrom and 3.2 degrees, respectively. Features of the protein that were recognized only in the revised model include: the disposition of water molecules within domain-domain interfaces; two ion pairs buried in domain-domain interfaces, one of which is a structural arginine around which the active-site phosphoserine loop is wound; the basic architecture of the active-site 'crevice', which is a groove in a 1 1/3-turn helix, open at both ends, that is produced by the interfacing of the four domains; the distorted hexacoordinate ligand sphere of the active-site Mg2+, where the enzymic phosphate group acts as a bidentate ligand; a pair of arginine residues in domain IV that form part of the enzymic phosphate-binding site (distal subsite) whose disposition in the two monomers of the asymmetric unit is affected unequally by distant crystallographic contacts; structural differences throughout domain IV, produced by these differing contacts, that may mimic solution differences induced by substrate binding; large differences in individually refined Debye-Waller thermal factors for corresponding main-chain atoms in monomers (1) and (2), suggesting a dynamic disorder within the crystal that may involve domain-size groups of residues; and a 'nucleophilic elbow' in the active site that resides in a topological environment differing from previous descriptions of this type of structure in other proteins.