4YET | pdb_00004yet

X-ray crystal structure of superoxide dismutase from Babesia bovis solved by Sulfur SAD

• PDB DOI: https://doi.org/10.2210/pdb4YET/pdb
• Entry: 4YET supersedes: 4K2W

• Classification: OXIDOREDUCTASE
• Organism(s): Babesia bovis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-24 Released: 2015-04-15 
• Deposition Author(s): Fairman, J.W., Clifton, M.C., Abendroth, J., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.176 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures.

Phan, I.Q., Davies, D.R., Moretti, N.S., Shanmugam, D., Cestari, I., Anupama, A., Fairman, J.W., Edwards, T.E., Stuart, K., Schenkman, S., Myler, P.J.

(2015) Acta Crystallogr F Struct Biol Commun 71: 615-621

• PubMed: 25961325 
• DOI: https://doi.org/10.1107/S2053230X15004185
• Primary Citation Related Structures: 
  4F2N, 4H3E, 4YET


• PubMed Abstract: 
  

  Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.

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Organizational Affiliation: 
• Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA.
CSIR-National Chemical Laboratory, Pune 411 008, India.
Departmento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.92 kDa 
• Atom Count: 3,628 
• Modeled Residue Count: 398 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B	203	Babesia bovis	Mutation(s): 0  Gene Names: Fe-SOD, BBOV_IV011480 EC: 1.15.1.1
UniProt
Find proteins for O15904 (Babesia bovis) Explore O15904  Go to UniProtKB:  O15904

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: 1.75 Å
• R-Value Free:  0.176 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.75	α = 90
b = 69.09	β = 90
c = 114.81	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Fairman, J.W., Clifton, M.C., Abendroth, J., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• This entry supersedes: 4K2W

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2015-06-03
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references, Derived calculations