3SDP

THE 2.1 ANGSTROMS RESOLUTION STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS OVALIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.1-A resolution structure of iron superoxide dismutase from Pseudomonas ovalis.

Stoddard, B.L.Howell, P.L.Ringe, D.Petsko, G.A.

(1990) Biochemistry 29: 8885-8893


  • PubMed Abstract: 
  • The 2.1-A resolution crystal structure of native uncomplexed iron superoxide dismutase (EC 1.15.1.1) from Pseudomonas ovalis was solved and refined to a final R factor of 24%. The dimeric structure contains one catalytic iron center per monomer with ...

    The 2.1-A resolution crystal structure of native uncomplexed iron superoxide dismutase (EC 1.15.1.1) from Pseudomonas ovalis was solved and refined to a final R factor of 24%. The dimeric structure contains one catalytic iron center per monomer with an asymmetric trigonal-bipyramidal coordination of protein ligands to the metal. Each monomer contains two domains, with the trigonal ligands (histidines 74 and 160; aspartate 156) contributed by the large domain and stabilized by an extended hydrogen-bonded network, including residues from opposing monomers. The axial ligand (histidine 26) is found on the small domain and does not participate extensively in the stabilizing H-bond network. The open axial coordination position of the iron is devoid of bound water molecules or anions. The metal is located 0.5 A out of the plane of the trigonal ligands toward histidine 26, providing a slightly skewed coordination away from the iron binding site. The molecule contains a glutamine residue in the active site which is conserved between all iron enzymes sequenced to data but which is conserved among all manganese SODs at a separate position in the sequence. This residue shows the same structural interactions in both cases, implying that iron and manganese SODs are second-site revertants of one another.


    Related Citations: 
    • The Structure of Iron Superoxide Dismutase from Pseudomonas Ovalis Bound to the Inhibitor Azide: Coordination Changes and Dynamics During Catalysis
      Stoddard, B.L.,Ringe, D.,Petsko, G.A.
      (1990) Protein Eng. 4: 113


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IRON SUPEROXIDE DISMUTASE
A, B
195Pseudomonas putidaMutation(s): 0 
Gene Names: sodB
EC: 1.15.1.1
Find proteins for P09223 (Pseudomonas putida)
Go to UniProtKB:  P09223
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.900α = 90.00
b = 49.100β = 106.80
c = 61.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROLSQrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance