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: 50.62 kDa 
• Atom Count: 3561 
• Modelled Residue Count: 395 
• Deposited Residue Count: 452 
• Unique protein chains: 1

2CW2

Crystal structure of Superoxide dismutase from P. Marinus

• PDB DOI: 10.2210/pdb2CW2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Perkinsus marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-16 Released: 2006-07-04 
• Deposition Author(s): Asojo, O.A., Schott, E.J., Vasta, G.R., Silva, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.216 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

Structures of PmSOD1 and PmSOD2, two superoxide dismutases from the protozoan parasite Perkinsus marinus

Asojo, O.A., Schott, E.J., Vasta, G.R., Silva, A.M.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1072-1075

• PubMed: 17077482 
• DOI: 10.1107/S1744309106040425
• Primary Citation of Related Structures:  
  2CW2, 2CW3


• PubMed Abstract: 
  

Perkinsus marinus, a facultative intracellular parasite of the eastern oyster Crassostrea virginica, is responsible for mass mortalities of oyster populations. P. marinus trophozoites survive and proliferate within oyster hemocytes, invading most tissues and fluids, thus causing a systemic infection that eventually kills the host. The phagocytosis of P. marinus trophozoites lacks a respiratory burst, suggesting that the parasite has mechanisms that actively abrogate the host's oxidative defense responses. One mechanism and the first line of defense against oxidative damage is the dismutation of superoxide radical to molecular oxygen and hydrogen peroxide by superoxide dismutases (SODs). P. marinus possesses two iron-cofactored SODs, PmSOD1 and PmSOD2. Here, the crystallization and X-ray structures of both PmSOD1 and PmSOD2 are presented.

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Organizational Affiliation: 

Pathology and Microbiology Department, University of Nebraska Medical Center, 986495 Nebraska Med Center, Omaha, NE 68198-6495, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
superoxide dismutase 1	A, B	226	Perkinsus marinus	Mutation(s): 0  Gene Names: SOD1 EC: 1.15.1.1
UniProt
Find proteins for Q8ISJ0 (Perkinsus marinus) Explore Q8ISJ0  Go to UniProtKB:  Q8ISJ0

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: 1.86 Å
• R-Value Free: 0.216 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.813	α = 90
b = 62.451	β = 95.54
c = 57.354	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-16 
• Released Date: 2006-07-04 
Deposition Author(s): Asojo, O.A., Schott, E.J., Vasta, G.R., Silva, A.M.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description