3DC6

Crystal Structure of a manganese superoxide dismutases from Caenorhabditis elegans


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 

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This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase [Mn] 1A,
B [auth C]
198Caenorhabditis elegansMutation(s): 0 
Gene Names: sod-2sdm-1F10D11.1
EC: 1.15.1.1
UniProt
Find proteins for P31161 (Caenorhabditis elegans)
Explore P31161 
Go to UniProtKB:  P31161
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31161
Protein Feature View
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  • Reference Sequence
Small Molecules
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 = 80.98α = 90
b = 80.98β = 90
c = 137.444γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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