Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 

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Motion of the DNA-binding domain with respect to the core of the diphtheria toxin repressor (DtxR) revealed in the crystal structures of apo- and holo-DtxR.

Pohl, E.Holmes, R.K.Hol, W.G.

(1998) J Biol Chem 273: 22420-22427

  • DOI: https://doi.org/10.1074/jbc.273.35.22420
  • Primary Citation of Related Structures:  
    1BI0, 1BI1, 1BI2, 1BI3

  • PubMed Abstract: 

    The diphtheria toxin repressor (DtxR) from Corynebacterium diphtheriae is a divalent metal-activated repressor of chromosomal genes that encode proteins responsible for siderophore-mediated iron uptake and also of the gene of certain corynebacteriophages that encodes diphtheria toxin. DtxR consists of two 25.3-kDa three-domain subunits and is a member of a family of related repressor proteins in several Gram-positive bacterial species, some of which are important human pathogens. In this paper, we report on the first high resolution crystal structures of apo-DtxR in two related space groups. In addition, crystal structures of Zn-DtxR were determined in the same two space groups. The resolutions of the structures range from 2.2 to 2.4 A. The four refined models of the apo- and the holo-repressor exhibit quite similar metal binding centers, which do, however, show higher thermal motion in the apo-structures. All four structures reported differ from each other in one important aspect. The N-terminal DNA-binding domain and the last 20 residues of the dimerization domain of each subunit move significantly with respect to the core of the DtxR dimer, which consists of residues 74-120 from both subunits. These results provide the first indication of a conformational change that may occur upon binding of the holo-repressor to DNA.

  • Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle, Washington 98195-7742, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
226Corynebacterium diphtheriaeMutation(s): 1 
Gene Names: DTXR
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore P0DJL7 
Go to UniProtKB:  P0DJL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJL7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.253 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.4α = 90
b = 63.4β = 90
c = 213.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations, Other