1YGZ

Crystal Structure of Inorganic Pyrophosphatase from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of inorganic pyrophosphatase from Helicobacter pylori.

Wu, C.A.Lokanath, N.K.Kim, D.Y.Park, H.J.Hwang, H.Y.Kim, S.T.Suh, S.W.Kim, K.K.

(2005) Acta Crystallogr.,Sect.D 61: 1459-1464

  • DOI: 10.1107/S0907444905025667
  • Also Cited By: 5LS0

  • PubMed Abstract: 
  • Inorganic pyrophosphatase (PPase) is a ubiquitous cytosolic enzyme which catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to orthophosphate (Pi). The crystal structure of inorganic pyrophosphatase from Helicobacter pylori (H-PPase) has been ...

    Inorganic pyrophosphatase (PPase) is a ubiquitous cytosolic enzyme which catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to orthophosphate (Pi). The crystal structure of inorganic pyrophosphatase from Helicobacter pylori (H-PPase) has been solved by MAD and refined to an R factor of 20.6% at 2.6 A resolution. The crystallographic asymmetric unit contains a homohexameric H-PPase arranged as a dimer of trimers. While most of the structural elements of PPases are highly conserved in H-PPase, some unique structural features are localized in the flexible loops near the active site, suggesting that the structural flexibility of these loops is required for the catalytic efficiency of PPase.


    Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inorganic pyrophosphatase
A, B, C, D, E, F
173Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: ppa
EC: 3.6.1.1
Find proteins for P56153 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56153
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 115.055α = 90.00
b = 115.055β = 90.00
c = 73.782γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance