1OBW

STRUCTURE OF INORGANIC PYROPHOSPHATASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of holo inorganic pyrophosphatase from Escherichia coli at 1.9 A resolution. Mechanism of hydrolysis.

Harutyunyan, E.H.Oganessyan, V.Y.Oganessyan, N.N.Avaeva, S.M.Nazarova, T.I.Vorobyeva, N.N.Kurilova, S.A.Huber, R.Mather, T.

(1997) Biochemistry 36: 7754-7760

  • DOI: 10.1021/bi962637u

  • PubMed Abstract: 
  • Crystalline holo inorganic pyrophosphatase from Escherichia coli was grown in the presence of 250 mM MgCl2. The crystal structure has been solved by Patterson search techniques and refined to an R-factor of 17.6% at 1.9 A resolution. The upper estima ...

    Crystalline holo inorganic pyrophosphatase from Escherichia coli was grown in the presence of 250 mM MgCl2. The crystal structure has been solved by Patterson search techniques and refined to an R-factor of 17.6% at 1.9 A resolution. The upper estimate of the root-mean-square error in atomic positions is 0.26 A. These crystals belong to space group P3(2)21 with unit cell dimensions a = b = 110.27 A and c = 78.17 A. The asymmetric unit contains a trimer of subunits, i.e., half of the hexameric molecule. In the central cavity of the enzyme molecule, three Mg2+ ions, each shared by two subunits of the hexamer, are found. In the active sites of two crystallographically independent subunits, two Mg2+ ions are bound. The second active site Mg2+ ion is missing in the third subunit. A mechanism of catalysis is proposed whereby a water molecule activated by a Mg2+ ion and Tyr 55 play essential roles.


    Related Citations: 
    • X-Ray Crystallographic Studies of Recombinant Inorganic Pyrophosphatase from Escherichia Coli
      Oganessyan, V.Yu.,Kurilova, S.A.,Vorobyeva, N.N.,Nazarova, T.I.,Popov, A.N.,Lebedev, A.A.,Avaeva, S.M.,Harutyunyan, E.H.
      (1994) FEBS Lett. 348: 301


    Organizational Affiliation

    Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russian Federation. emil@protein.crystal.msk.ru




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INORGANIC PYROPHOSPHATASE
A, B, C
175Escherichia coli (strain K12)Gene Names: ppa
EC: 3.6.1.1
Find proteins for P0A7A9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7A9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.176 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.300α = 90.00
b = 110.300β = 90.00
c = 78.200γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance