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STRUCTURE OF THE ADP COMPLEX OF THE 3-PHOSPHOGLYCERATE KINASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.65 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Work: 0.156 

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Literature

Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A.

Davies, G.J.Gamblin, S.J.Littlechild, J.A.Dauter, Z.Wilson, K.S.Watson, H.C.

(1994) Acta Crystallogr.,Sect.D 50: 202-209

  • DOI: 10.1107/S0907444993011138

  • PubMed Abstract: 
  • The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 f ...

    The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 for all data between 10.0 and 1.65 A resolution, using data collected on the Hendrix-Lentfer imaging plate at the EMBL outstation in Hamburg. The r.m.s. deviations from stereochemical ideality are 0.010 and 0.011 A for bonds and planes, respectively. Although crystallized in the presence of the nucleotide product MgATP, the high-resolution structure reveals the bound nucleotide to be MgADP reflecting the low intrinsic ATPase activity of PGK. Although the two domains of this enzyme are found to be some 4.5 degrees closer together than is found in the yeast and horse-muscle apo-enzyme structures, this structure represents the 'open' rather than the 'closed', catalytically competent form, of the enzyme.


    Related Citations: 
    • Purification, Crystallisation and Preliminary X-Ray Analysis of the 3-Phosphoglycerate Kinase from Bacillus Stearothermophilus
      Davies, G.J.,Gamblin, S.J.,Littlechild, J.A.,Watson, H.C.
      (1992) J.Mol.Biol. 227: 1263
    • Sequence and Expression of the Gene Encoding 3-Phosphoglycerate Kinase from Bacillus Stearothermophilus
      Davies, G.J.,Littlechild, J.A.,Watson, H.C.,Hall, L.
      (1991) Gene 109: 39
    • The Structure of a Thermally Stable 3-Phosphoglycerate Kinase and a Comparison with its Mesophilic Equivalent
      Davies, G.J.,Gamblin, S.J.,Littlechild, J.A.,Watson, H.C.
      (1993) Proteins 15: 283


    Organizational Affiliation

    Department of Biochemistry, School of Medical Sciences, University of Bristol, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-PHOSPHOGLYCERATE KINASE
A
394Geobacillus stearothermophilusGene Names: pgk
EC: 2.7.2.3
Find proteins for P18912 (Geobacillus stearothermophilus)
Go to UniProtKB:  P18912
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.410α = 90.00
b = 73.930β = 99.80
c = 68.570γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance