Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44.68 kDa 
• Atom Count: 3635 
• Modelled Residue Count: 395 
• Deposited Residue Count: 396 
• Unique protein chains: 1

3DC6

Crystal Structure of a manganese superoxide dismutases from Caenorhabditis elegans

• PDB DOI: 10.2210/pdb3DC6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-03 Released: 2009-06-09 
• Deposition Author(s): Trinh, C.H., Hunter, T., Stewart, E.E., Phillips, S.E.V., Hunter, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans

Trinh, C.H., Hunter, T., Stewart, E.E., Phillips, S.E., Hunter, G.J.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 1110-1114

• PubMed: 19052361 
• DOI: 10.1107/S1744309108037056
• Primary Citation of Related Structures:  
  3DC5, 3DC6


• PubMed Abstract: 
  

Caenorhabditis elegans expresses two manganese superoxide dismutase enzymes (MnSOD-2 and MnSOD-3) that are targeted to the mitochondrion. MnSOD-2 is constitutively expressed, while synthesis of MnSOD-3 is inducible. The structures of these two mononuclear metalloenzymes have been determined to 1.8 and 1.7 A resolution, respectively. Pink crystals formed in space group P4(1)2(1)2 for each, with unit-cell parameters a = b = 81.0, c = 137.4 A for MnSOD-2 and a = b = 81.8, c = 136.0 A for MnSOD-3. The final structure of MnSOD-3 was refined to R = 21.6% and R(free) = 26.2% at 293 K, and R = 18.9% and R(free) = 22.6% at 100 K, while that of MnSOD-2 was refined to R = 16.9% and R(free) = 20.1% at 100 K. The asymmetric unit cell is comprised of two subunits. The resulting structures are very similar to that of human MnSOD and form a tetramer corresponding to a dimer of dimers. The subunit interface between dimers is comprised of two four-helix bundles that stabilize the biologically significant homotetramer.

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Organizational Affiliation: 

Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn] 1	A, B [auth C]	198	Caenorhabditis elegans	Mutation(s): 0  Gene Names: sod-2, sdm-1, F10D11.1 EC: 1.15.1.1
UniProt
Find proteins for P31161 (Caenorhabditis elegans) Explore P31161  Go to UniProtKB:  P31161

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.98	α = 90
b = 80.98	β = 90
c = 137.444	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-03 
• Released Date: 2009-06-09 
Deposition Author(s): Trinh, C.H., Hunter, T., Stewart, E.E., Phillips, S.E.V., Hunter, G.J.

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance