3CEI

Crystal Structure of Superoxide Dismutase from Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of the superoxide dismutase from Helicobacter pylori reveals a structured C-terminal extension

Esposito, L.Seydel, A.Aiello, R.Sorrentino, G.Cendron, L.Zanotti, G.Zagari, A.

(2008) Biochim.Biophys.Acta 1784: 1601-1606

  • DOI: 10.1016/j.bbapap.2008.04.024

  • PubMed Abstract: 
  • Superoxide dismutases (SODs) are key enzymes for fighting oxidative stress. Helicobacter pylori produces a single SOD (HpSOD) which contains iron. The structure of this antioxidant protein has been determined at 2.4 A resolution. It is a dimer of two ...

    Superoxide dismutases (SODs) are key enzymes for fighting oxidative stress. Helicobacter pylori produces a single SOD (HpSOD) which contains iron. The structure of this antioxidant protein has been determined at 2.4 A resolution. It is a dimer of two identical subunits with one iron ion per monomer. The protein shares 53% sequence identity with the corresponding enzyme from Escherichia coli. The model is compared with those of other dimeric Fe-containing SODs. HpSOD shows significant differences in relation to other SODs, the most important being an extended C-terminal tail. This structure provides a model for closely related sequences from species such as Campylobacter, where no structures are currently known. The structure of extended carboxyl termini is discussed in light of putative functions it may serve.


    Organizational Affiliation

    Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134, Naples, Italy. luciana.esposito@unina.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase
A, B
213Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: sodB
EC: 1.15.1.1
Find proteins for P43312 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P43312
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.201 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.716α = 90.00
b = 108.716β = 90.00
c = 158.031γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance