4JYY | pdb_00004jyy

Crystal structure of the azide and iron substituted Clostrium difficile SOD2 complex

• PDB DOI: https://doi.org/10.2210/pdb4JYY/pdb

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


• Deposited: 2013-04-01 Released: 2014-04-02 
• Deposition Author(s): Li, W., Ying, T.L., Wang, C.L., Zhao, Y., Wang, H.F., Tan, X.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.198 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the azide and iron substituted Clostrium difficile SOD2 complex

Li, W., Ying, T.L., Wang, C.L., Zhao, Y., 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: 24.38 kDa 
• Atom Count: 1,808 
• Modeled 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 EC: 1.15.1.1
UniProt
Find proteins for Q186I6 (Clostridioides difficile (strain 630)) Explore Q186I6  Go to UniProtKB:  Q186I6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
AZI	C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.198 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.375	α = 90
b = 80.375	β = 90
c = 250.532	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Li, W., Ying, T.L., Wang, C.L., Zhao, Y., Wang, H.F., Tan, X.S.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description