Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.30 kDa 
• Atom Count: 3666 
• Modelled Residue Count: 423 
• Deposited Residue Count: 426 
• Unique protein chains: 1

3CEI

Crystal Structure of Superoxide Dismutase from Helicobacter pylori

• PDB DOI: 10.2210/pdb3CEI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-29 Released: 2008-06-10 
• Deposition Author(s): Esposito, L., Seydel, A., Aiello, R., Sorrentino, G., Cendron, L., Zanotti, G., Zagari, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.201 

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

• PubMed: 18502213 
• DOI: 10.1016/j.bbapap.2008.04.024
• Primary Citation of Related Structures:  
  3CEI


• 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 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.

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Organizational Affiliation: 

Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134, Naples, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B	213	Helicobacter pylori	Mutation(s): 0  Gene Names: sod EC: 1.15.1.1
UniProt
Find proteins for P43312 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P43312  Go to UniProtKB:  P43312

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	C [auth A], E [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.201 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.716	α = 90
b = 108.716	β = 90
c = 158.031	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-29 
• Released Date: 2008-06-10 
Deposition Author(s): Esposito, L., Seydel, A., Aiello, R., Sorrentino, G., Cendron, L., Zanotti, G., Zagari, A.

Revision History  

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