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 PQS (software)

Macromolecule Content

• Total Structure Weight: 42.93 kDa 
• Atom Count: 3228 
• Modelled Residue Count: 386 
• Deposited Residue Count: 388 
• Unique protein chains: 1

2W7W

The crystal structure of iron superoxide dismutase from Aliivibrio salmonicida.

• PDB DOI: 10.2210/pdb2W7W/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aliivibrio salmonicida LFI1238
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-06 Released: 2009-02-17 
• Deposition Author(s): Pedersen, H.L., Willassen, N.P., Leiros, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.

Pedersen, H.L., Willassen, N.P., Leiros, I.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 84-92

• PubMed: 19193992 
• DOI: 10.1107/S1744309109001110
• Primary Citation of Related Structures:  
  2W7W


• PubMed Abstract: 
  

Superoxide dismutases (SODs) are metalloenzymes that catalyse the dismutation of the superoxide radical anion into O(2) and H(2)O(2) in a two-step reaction. The crystal structure of the iron superoxide dismutase from the cold-adapted and fish-pathogenic bacterium Aliivibrio salmonicida (asFeSOD) has been determined and refined to 1.7 A resolution. The protein has been characterized and compared with the closely related homologous iron superoxide dismutase from the mesophilic Escherichia coli (ecFeSOD) in an attempt to rationalize its environmental adaptation. ecFeSOD shares 75% identity with asFeSOD. Compared with the mesophilic FeSOD, the psychrophilic FeSOD has distinct temperature differences in residual activity and thermostability that do not seem to be related to structural differences such as intramolecular or intermolecular ion bonds, hydrogen bonds or cavity sizes. However, an increased net negative charge on the surface of asFeSOD may explain its lower thermostability compared with ecFeSOD. Activity measurements and differential scanning calorimetry measurements revealed that the psychrophilic asFeSOD had a thermostability that was significantly higher than the optimal growth temperature of the host organism.

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Organizational Affiliation: 

Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE [FE]	A, B	194	Aliivibrio salmonicida LFI1238	Mutation(s): 0  Gene Names: sodB, VSAL_I1858 EC: 1.15.1.1
UniProt
Find proteins for B6ENP9 (Aliivibrio salmonicida (strain LFI1238)) Explore B6ENP9  Go to UniProtKB:  B6ENP9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.72	α = 90
b = 70.72	β = 90
c = 170.25	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-06 
• Released Date: 2009-02-17 
Deposition Author(s): Pedersen, H.L., Willassen, N.P., Leiros, I.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-02-06
  Changes: Data collection, Database references, Experimental preparation