3PMG

STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY

Replaces:  2PMG

Summary for 3PMG

• Entry DOI: 10.2210/pdb3pmg/pdb
• Descriptor: Phosphoglucomutase-1, MAGNESIUM ION (3 entities in total)
• Functional Keywords: phosphotransferase, isomerase
• Biological source: Oryctolagus cuniculus (rabbit)
• Total number of polymer chains: 2
• Total formula weight: 123208.41

Authors

Ray Junior, W.J.,Liu, Y.,Baranidharan, S. (deposition date: 1995-03-02, release date: 1995-12-07, Last modification date: 2024-10-16)

Primary citation

Liu, Y.,Ray, W.J.,Baranidharan, S.
Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution.
Acta Crystallogr.,Sect.D, 53:392-405, 1997

PubMed Abstract: Data between 6.0 and 2.4 A resolution, collected at 253 K, wer used to refine a revised atomic model of muscle phosphoglucomutase: final crystallographic R factor = 16.3% (Rfree = 19.1%); final r.m.s. deviations from ideal bond lengths and angles = 0.018 A 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.

PubMed: 15299905
DOI: 10.1107/S0907444997000875

Experimental method

X-RAY DIFFRACTION (2.4 Å)