6EX4 | pdb_00006ex4

Staphylococcus aureus cambialistic superoxide dismutase SodM

• PDB DOI: https://doi.org/10.2210/pdb6EX4/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: 2.40 Å
• R-Value Free: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.176 (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)

Macromolecule Content 

• Total Structure Weight: 46.25 kDa 
• Atom Count: 3,345 
• Modeled Residue Count: 396 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A, B	199	Staphylococcus aureus	Mutation(s): 0  Gene Names: sodA, sodM, BER48_000119, BN1321_40056, CEJ93_07215, ERS072738_00830, ERS072840_00559, ERS073583_02338, ERS074020_00889, HMPREF3211_00238 EC: 1.15.1.1
UniProt
Find proteins for Q2G261 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G261  Go to UniProtKB:  Q2G261

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: 2.40 Å
• R-Value Free:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.954	α = 90
b = 141.954	β = 90
c = 46.159	γ = 120

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