1S4I

Crystal structure of a SOD-like protein from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.

Banci, L.Bertini, I.Calderone, V.Cramaro, F.Del Conte, R.Fantoni, A.Mangani, S.Quattrone, A.Viezzoli, M.S.

(2005) Proc.Natl.Acad.Sci.Usa 102: 7541-7546

  • DOI: 10.1073/pnas.0502450102
  • Primary Citation of Related Structures:  
  • Also Cited By: 1XTM, 1XTL

  • PubMed Abstract: 
  • Little is known about prokaryotic homologs of Cu,Zn superoxide dismutase (SOD), an enzyme highly conserved among eukaryotic species. In 138 Archaea and Bacteria genomes, 57 of these putative homologs were found, 11 of which lack at least one of the m ...

    Little is known about prokaryotic homologs of Cu,Zn superoxide dismutase (SOD), an enzyme highly conserved among eukaryotic species. In 138 Archaea and Bacteria genomes, 57 of these putative homologs were found, 11 of which lack at least one of the metal ligands. Both the solution and the crystal structures of the SOD-like protein from Bacillus subtilis, lacking two Cu ligands and found to be enzymatically inactive, were determined. In solution, the protein is monomeric. The available nuclear Overhauser effects, together with chemical-shift index values, allowed us to define and to recognize the typical Cu,Zn SOD Greek beta-barrel but with largely unstructured loops (which, therefore, sample a wide range of conformations). On the contrary, in the crystal structure (obtained in the presence of slight excess of Zn), the protein is well structured and organized in covalent dimers held by a symmetric bridge consisting of a Zn ion bound to an Asp-His dyad in a tetrahedral geometry. Couples of dimers held by hydrophobic interactions and H bonds are further organized in long chains. The order/disorder transition is discussed in terms of metal binding and physical state.


    Organizational Affiliation

    Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto, Florence, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
superoxide dismutase-like protein yojM
B, A, C, D
175Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yojM
Find proteins for O31851 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31851
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.225α = 84.35
b = 61.108β = 76.02
c = 64.915γ = 90.42
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHARPphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance