3TJT

Crystal Structure Analysis of the superoxide dismutase from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb3TJT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-25 Released: 2012-08-29 
• Deposition Author(s): Li, W., Lei, C., Ying, T.L., Wang, H.F., Tan, X.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Crystal Structure of the superoxide dismutase from Clostridium difficile

Li, W., Lei, C., Ying, T.L., Wang, H.F., Tan, X.S.

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)

Macromolecule Content

• Total Structure Weight: 24.34 kDa 
• Atom Count: 2,031 
• Modelled Residue Count: 202 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase	A	208	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_16310, sodA, YP_001088132.1 EC: 1.15.1.1
UniProt
Find proteins for Q186I6 (Clostridioides difficile (strain 630)) Explore Q186I6  Go to UniProtKB:  Q186I6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.399	α = 90
b = 80.399	β = 90
c = 251.631	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Li, W., Lei, C., Ying, T.L., Wang, H.F., Tan, X.S.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description