Cambialistic superoxide dismutase from Porphyromonas gingivalis

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

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This is version 1.7 of the entry. See complete history


Crystal Structure of Cambialistic Superoxide Dismutase from Porphyromonas Gingivalis

Sugio, S.Hiraoka, B.Y.Yamakura, F.

(2000) Eur J Biochem 267: 3487

  • DOI: https://doi.org/10.1046/j.1432-1327.2000.01373.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of cambialistic superoxide dismutase (SOD) from Porphyromonas gingivalis, which exhibits full activity with either Fe or Mn at the active site, has been determined at 1.8-A resolution by molecular replacement and refined to a crystallographic R factor of 17.9% (Rfree 22.3%). The crystals belong to the space group P212121 (a = 75.5 A, b = 102.7 A, c = 99.6 A) with four identical subunits in the asymmetric unit. Each pair of subunits forms a compact dimer, but not a tetramer, with 222 point symmetry. Each subunit has 191 amino-acid residues most of which are visible in electron density maps, and consists of seven alpha helices and one three-stranded antiparallel beta sheet. The metal ion, a 3 : 1 mixture of Fe and Mn, is coordinated with five ligands (His27, His74, His161, Asp157, and water) arranged at the vertices of a trigonal bipyramid. Although the overall structural features, including the metal coordination geometry, are similar to those found in other single-metal containing SODs, P. gingivalis SOD more closely resembles the dimeric Fe-SODs from Escherichia coli rather than another cambialistic SOD from Propionibacterium shermanii, which itself is rather similar to other tetrameric SODs.

  • Organizational Affiliation

    Yokohama Research Center, Mitsubishi Chemical Corporation, Aoba, Yokohama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
191Porphyromonas gingivalisMutation(s): 0 
Find proteins for P19665 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore P19665 
Go to UniProtKB:  P19665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19665
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.47α = 90
b = 102.66β = 90
c = 99.59γ = 90
Software Package:
Software NamePurpose
PROCESSdata reduction
PROCESSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-21
    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: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-04-10
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.7: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description