1QNN

Cambialistic superoxide dismutase from Porphyromonas gingivalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Crystal Structure of Cambialistic Superoxide Dismutase from Porphyromonas Gingivalis

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

(2000) Eur.J.Biochem. 267: 3487

  • Also Cited By: 1UES, 1UER

  • 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 cr ...

    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.


    Related Citations: 
    • Characterization of Superoxide Dismutase Purified from Either Anaerobically Maintained or Aerated Bacteroides Gingivalis
      Amano, A.,Shizukuishi, S.,Tamagawa, H.,Iwakura, K.,Tsunasawa, S.,Tsunemitsu, S.
      (1990) J.Bacteriol. 172: 1457
    • Inactivation and Destruction of Conserved Trp159 of Fe-Superoxide Dismutase from Porphyromonas Gingivalis by Hydrogen Peroxide
      Yamakura, F.,Rardin, R.L.,Petsko, G.A.,Ringe, D.,Hiraoka, B.Y.,Nakayama, K.,Fujimura, T.,Taka, H.,Murayama, K.
      (1998) Eur.J.Biochem. 253: 49
    • The Primary Structure of Superoxide Dismutase Purified from Anaerobically Maintained Bacteroides Gingivalis
      Amano, A.,Shizukuishi, S.,Tsunemitsu, A.,Maekawa, K.,Tsunemitsu, S.
      (1990) FEBS Lett. 272: 217


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUPEROXIDE DISMUTASE
A, B, C, D
191Porphyromonas gingivalis (strain ATCC BAA-308 / W83)Mutation(s): 0 
Gene Names: sodB
EC: 1.15.1.1
Find proteins for P19665 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  P19665
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.470α = 90.00
b = 102.660β = 90.00
c = 99.590γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection
  • Version 1.4: 2019-03-06
    Type: Data collection, Experimental preparation
  • Version 1.5: 2019-04-10
    Type: Data collection, Source and taxonomy
  • Version 1.6: 2019-05-08
    Type: Data collection, Experimental preparation