1YGZ | pdb_00001ygz

Crystal Structure of Inorganic Pyrophosphatase from Helicobacter pylori

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.204 (DCC) 

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This is version 1.3 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 D Biol Crystallogr 61: 1459-1464

  • DOI: https://doi.org/10.1107/S0907444905025667
  • Primary Citation of Related Structures:  
    1YGZ

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inorganic pyrophosphatase
A, B, C, D, E
A, B, C, D, E, F
173Helicobacter pylori 26695Mutation(s): 4 
EC: 3.6.1.1
UniProt
Find proteins for P56153 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56153 
Go to UniProtKB:  P56153
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56153
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.055α = 90
b = 115.055β = 90
c = 73.782γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary