3EVK | pdb_00003evk

Crystal structure of the metal-bound superoxide dismutase from Pyrobaculum aerophilum

• PDB DOI: https://doi.org/10.2210/pdb3EVK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pyrobaculum aerophilum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-13 Released: 2009-08-25 
• Deposition Author(s): Lee, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Metal-bound Superoxide Dismutase from Pyrobaculum aerophilum and Comparison with the Metal-free Form

Lee, S.

(2008) Bull Korean Chem Soc 29: 2399-2402

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.26 kDa 
• Atom Count: 7,037 
• Modeled Residue Count: 844 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Fe]	A, B, C, D	222	Pyrobaculum aerophilum	Mutation(s): 0  Gene Names: sod, PAE0274 EC: 1.15.1.1
UniProt
Find proteins for O93724 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore O93724  Go to UniProtKB:  O93724

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth B], G [auth C], H [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.909	α = 90
b = 94.909	β = 90
c = 171.89	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Lee, S.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description