3PMG image
Deposition Date 1995-03-02
Release Date 1995-12-07
Last Version Date 2024-10-16
Entry Detail
PDB ID:
3PMG
Keywords:
Title:
STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Phosphoglucomutase-1
Gene (Uniprot):PGM1
Chain IDs:A, B
Chain Length:561
Number of Molecules:2
Biological Source:Oryctolagus cuniculus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER PHOSPHOSERINE
Ligand Molecules
Primary Citation
Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution.
Acta Crystallogr.,Sect.D 53 392 405 (1997)
PMID: 15299905 DOI: 10.1107/S0907444997000875

Abstact

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.

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Primary Citation of related structures