6D52 | pdb_00006d52

Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6D52/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-19 Released: 2019-05-15 
• Deposition Author(s): Newhouse IX, P.W., Forest, K.T., Satyshur, K.A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.184 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6 Angstrom resolution

Newhouse IX, P.W., Satyshur, K.A., Forest, K.T., Slauch, J.M.

To be published.

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 Evidence: SAXS, gel filtration, light scattering

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: 70.27 kDa 
• Atom Count: 5,317 
• Modeled Residue Count: 627 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn] 1	A [auth B], B [auth D], C, D [auth A]	165	Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74	Mutation(s): 0  Gene Names: sodC1, sodC, STM474_1035 EC: 1.15.1.1
UniProt
Find proteins for E8XDJ8 (Salmonella typhimurium (strain 4/74)) Explore E8XDJ8  Go to UniProtKB:  E8XDJ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth B], G [auth D], I [auth C], K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	F [auth B], H [auth D], J [auth C], L [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.184 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.53	α = 90
b = 68.571	β = 90
c = 122.172	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Newhouse IX, P.W., Forest, K.T., Satyshur, K.A.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	IOS 1353674
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM007215

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary