2WWN | pdb_00002wwn

Yersinia pseudotuberculosis Superoxide Dismutase C with bound Azide

• PDB DOI: https://doi.org/10.2210/pdb2WWN/pdb
• Entry: 2WWN supersedes: 2WN1

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pseudotuberculosis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-10-26 Released: 2010-11-03 
• Deposition Author(s): Basak, A.K., Duffield, M.L., Naylor, C.E., Huyet, J., Titball, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.232 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Yersinia Pseudotuberculosis Superoxide Dismutase (Sodc)

Huyet, J., Naylor, C.E., Titball, R.W., Bullifent, H., Walker, N., Jones, H.E., Duffied, M.L., Basak, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.48 kDa 
• Atom Count: 2,368 
• Modeled Residue Count: 314 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUPEROXIDE DISMUTASE [CU-ZN]	A, B	169	Yersinia pseudotuberculosis	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for Q66ED7 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66ED7  Go to UniProtKB:  Q66ED7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	H [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
AZI	K [auth B], L [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.232 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.561	α = 90
b = 96.561	β = 90
c = 81.716	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Basak, A.K., Duffield, M.L., Naylor, C.E., Huyet, J., Titball, R.W.
• This entry supersedes: 2WN1

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary