1LXT

STRUCTURE OF PHOSPHOTRANSFERASE PHOSPHOGLUCOMUTASE FROM RABBIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of rabbit muscle phosphoglucomutase refined at 2.4 A resolution.

Liu, Y.Ray, W.J.Baranidharan, S.

(1997) Acta Crystallogr.,Sect.D 53: 392-405

  • DOI: 10.1107/S0907444997000875
  • Primary Citation of Related Structures:  3PMG

  • 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 ...

    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.


    Related Citations: 
    • Structural Changes at the Metal Ion Binding Site During the Phosphoglucomutase Reaction
      Ray Junior, W.J.,Post, C.B.,Liu, Y.,Rhyu, G.I.
      (1993) Biochemistry 32: 48
    • The Catalytic Activity of Muscle Phosphoglucomutase in the Crystalline Phase
      Ray Junior, W.J.
      (1986) J.Biol.Chem. 261: 275
    • The Structure of Rabbit Muscle Phosphoglucomutase at Intermediate Resolution
      Lin, Z.,Konno, M.,Abad-Zapatero, C.,Wierenga, R.,Murthy, M.R.,Ray Junior, W.J.,Rossmann, M.G.
      (1986) J.Biol.Chem. 261: 264
    • The Crystal Structure of Muscle Phosphoglucomutase Refined at 2.7-Angstrom Resolution
      Dai, J.B.,Liu, Y.,Ray Junior, W.J.,Konno, M.
      (1992) J.Biol.Chem. 267: 6322


    Organizational Affiliation

    The Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLUCOMUTASE (DEPHOSPHO FORM)
A, B
561Oryctolagus cuniculusGene Names: PGM1
EC: 5.4.2.2
Find proteins for P00949 (Oryctolagus cuniculus)
Go to Gene View: PGM1
Go to UniProtKB:  P00949
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 174.420α = 90.00
b = 174.420β = 90.00
c = 101.120γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
XDSdata reduction
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance