Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 24.43 kDa 
• Atom Count: 1819 
• Modelled Residue Count: 211 
• Deposited Residue Count: 212 
• Unique protein chains: 1

1COJ

FE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM

• PDB DOI: 10.2210/pdb1COJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aquifex pyrophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1999-05-28 Released: 1999-06-14 
• Deposition Author(s): Lim, J.H., Yu, Y.G., Kim, S.-H., Cho, S.-J., Ahn, B.Y., Han, Y.S., Cho, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 

Literature

The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution: structural basis for thermostability.

Lim, J.H., Yu, Y.G., Han, Y.S., Cho, S., Ahn, B.Y., Kim, S.H., Cho, Y.

(1997) J Mol Biol 270: 259-274

• PubMed: 9236127 
• DOI: 10.1006/jmbi.1997.1105
• Primary Citation of Related Structures:  
  1COJ


• PubMed Abstract: 
  

Superoxide dismutase (SOD) from Aquifex pyrophilus, a hyperthermophilic bacterium, is an extremely heat-stable enzyme that maintains about 70% of its activity after heat treatment for 60 minutes at 100 degrees C. To understand the molecular basis of thermostability of this enzyme, we have determined the crystal structure of A. pyrophilus superoxide dismutase (Ap SOD), an Fe containing homotetrameric enzyme, at 1.9 A resolution, and compared it with SOD structures from a mesophile and a thermophile, and other enzyme structures from other hyperthermophiles. The structure has been refined to a crystallographic R-factor (I > 2sigma) of 17.0% and R-free (I > 2sigma) of 19.9%. While the overall structure of the Ap SOD monomer is similar to the other SODs, significant conformational differences are observed in a highly variable loop region and the C-terminal helix. The conformational differences in these regions alter the subunit arrangement of this enzyme and generate a very compact tetramer. Structural comparisons of three SODs have revealed that Ap SOD has some stabilizing features at both the tertiary and the quaternary structural level: The Ap SOD monomer contains a large number of ion-pairs and the Ap SOD tetramer has a dramatically increased buried surface area per monomer. Comparisons of the Ap SOD structure with that of other known enzymes from hyperthermophiles reveal that the increased number of intrasubunit ion-pairs is a common feature.

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Organizational Affiliation: 

Structural Biology Center, Korea Institute of Science and Technology, Seoul, South Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SUPEROXIDE DISMUTASE)	A	212	Aquifex pyrophilus	Mutation(s): 0  Gene Names: sodB, sod EC: 1.15.1.1
UniProt
Find proteins for Q9X6W9 (Aquifex pyrophilus) Explore Q9X6W9  Go to UniProtKB:  Q9X6W9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.170 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 75.63	β = 90
c = 87.3	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-28 
• Released Date: 1999-06-14 
Deposition Author(s): Lim, J.H., Yu, Y.G., Kim, S.-H., Cho, S.-J., Ahn, B.Y., Han, Y.S., Cho, Y.

Revision History  

• Version 1.0: 1999-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance