Crystal structure of omega transcriptional repressor at 1.5A resolution

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution.

Murayama, K.Orth, P.de la Hoz, A.B.Alonso, J.C.Saenger, W.

(2001) J Mol Biol 314: 789-796

  • DOI: https://doi.org/10.1006/jmbi.2001.5157
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 71 amino acid residue omega protein encoded by the Streptococcus pyogenes non-conjugative plasmid pSM19035 is a transcriptional repressor that regulates expression of genes for copy number control and stable maintenance of plasmids. The crystal structure of omega protein has been determined by multiple isomorphous replacement, including anomalous scattering and refined to an R-factor of 21.1 % (R(free)=23.2 %) at 1.5 A resolution. Two monomers related by a non-crystallographic 2-fold axis form a homodimer that occupies the asymmetric unit. Each polypeptide chain is folded into two alpha-helices and one beta-strand forming an antiparallel beta-ribbon in the homodimer. The N-terminal regions (1-23 and 1-22 in subunits I and II, respectively) are not defined in the electron density due to proteolysis of the N-terminal 20 amino acid residues during crystallisation and partial disorder. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognizing the major groove of operator DNA; according to a modelled omega protein-DNA complex, residues Arg31 and Arg31' on the beta-ribbon are in positions to interact with a nucleobase, especially guanine.

  • Organizational Affiliation

    Institut für Kristallographie Freie Universität Berlin, Takustrasse 6, Berlin, D-14195, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
omega transcriptional repressor
A, B
71Streptococcus pyogenesMutation(s): 0 
Gene Names: omega
Find proteins for Q57468 (Streptococcus pyogenes)
Explore Q57468 
Go to UniProtKB:  Q57468
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57468
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.1α = 90
b = 46.1β = 90
c = 88.3γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance