1MY6 | pdb_00001my6

The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics

• PDB DOI: https://doi.org/10.2210/pdb1MY6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermosynechococcus vestitus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-10-03 Released: 2003-07-29 
• Deposition Author(s): Yoshida, S.M., Cascio, D., Sawaya, M.R., Yeates, T.O., Kerfeld, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus.

Kerfeld, C.A., Yoshida, S., Tran, K.T., Yeates, T.O., Cascio, D., Bottin, H., Berthomieu, C., Sugiura, M., Boussac, A.

(2003) J Biol Inorg Chem 8: 707-714

• PubMed: 12827458 
• DOI: https://doi.org/10.1007/s00775-003-0469-0
• Primary Citation Related Structures: 
  1MY6


• PubMed Abstract: 
  

  The iron-containing superoxide dismutase (FeSOD) from the thermophilic cyanobacterium Thermosynechococcus elongatus has been isolated. The protein crystallizes readily and we have determined the structure to 1.6 A resolution. This is the first structural characterization of an FeSOD isolated from a cyanobacterium and one of the highest resolution FeSOD structures determined to date. The activity of the T. elongatus FeSOD has been measured both at 25 degrees C and 50 degrees C and it has been spectroscopically characterized. The T. elongatus FeSOD EPR spectra at pH 5.1, 7.5 and 10.0 are similar. This indicates that no change in the geometry of the Fe(III) site occurs over a wide range of pH. This is in contrast to the other FeSODs described in the literature.

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Organizational Affiliation: 
• Molecular Biology Institute, UCLA, Box 951570, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.32 kDa 
• Atom Count: 3,695 
• Modeled Residue Count: 396 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron (III) Superoxide Dismutase	A, B	199	Thermosynechococcus vestitus	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for Q8DIR2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIR2  Go to UniProtKB:  Q8DIR2

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: 1.60 Å
• R-Value Free:  0.232 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.749	α = 90
b = 63.644	β = 110.45
c = 74.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-29 
Deposition Author(s): Yoshida, S.M., Cascio, D., Sawaya, M.R., Yeates, T.O., Kerfeld, C.A.

Revision History  

• Version 1.0: 2003-07-29
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description