Macromolecule Content

Total Structure Weight: 91.18 kDa
Atom Count: 6412
Modelled Residue Count: 776
Deposited Residue Count: 796
Unique protein chains: 1

6EX3

Staphylococcus aureus superoxide dismutase SodA

PDB DOI: 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267
R-Value Work: 0.201
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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: 10.1038/s41467-020-16478-0

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A0J3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267
R-Value Work: 0.201
R-Value Observed: 0.204
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2017-11-07
Released Date: 2018-11-21

Deposition Author(s):

Barwinska-Sendra, A.

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

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2020-06-10
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.