6EX3

Staphylococcus aureus superoxide dismutase SodA

• PDB DOI: https://doi.org/10.2210/pdb6EX3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-07 Released: 2018-11-21 
• Deposition Author(s): Barwinska-Sendra, A., Basle, A., Waldron, K.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.267 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

An evolutionary path to altered cofactor specificity in a metalloenzyme

Barwinska-Sendra, A., Garcia, Y.M., Sendra, K., Basle, A., Mackenzie, E.S., Tarrant, E., Card, P., Tabares, L.C., Bicep, C., Un, S., Kehl-Fie, T.E., Waldron, K.J.

(2020) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-020-16478-0

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.18 kDa 
• Atom Count: 6,412 
• Modelled Residue Count: 776 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B, C, D	199	Staphylococcus aureus	Mutation(s): 0  Gene Names: sodA, BER48_001496, BN1321_260190, CEJ93_06715, ERS072738_01312, ERS072840_00871, ERS073583_00205, ERS074020_01135, HMPREF3211_01704 EC: 1.15.1.1
UniProt
Find proteins for P0A0J3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P0A0J3  Go to UniProtKB:  P0A0J3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.267 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.557	α = 90
b = 66.381	β = 98.72
c = 108.311	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Barwinska-Sendra, A., Basle, A., Waldron, K.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--
Wellcome Trust	United Kingdom	098375/Z/12/Z

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description