1XCV | pdb_00001xcv

Crystal Structure Of (H79AC102D)Dtxr complexed with Nickel(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.300 (Depositor) 
  • R-Value Work: 
    0.279 (Depositor) 
  • R-Value Observed: 
    0.279 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Mechanism of metal ion activation of the diphtheria toxin repressor DtxR.

D'Aquino, J.A.Tetenbaum-Novatt, J.White, A.Berkovitch, F.Ringe, D.

(2005) Proc Natl Acad Sci U S A 102: 18408-18413

  • DOI: https://doi.org/10.1073/pnas.0500908102
  • Primary Citation Related Structures: 
    1XCV

  • PubMed Abstract: 

    The diphtheria toxin repressor (DtxR) is a metal ion-activated transcriptional regulator that has been linked to the virulence of Corynebacterium diphtheriae. Structure determination has shown that there are two metal ion binding sites per repressor monomer, and site-directed mutagenesis has demonstrated that binding site 2 (primary) is essential for recognition of the target DNA repressor, leaving the role of binding site 1 (ancillary) unclear. Calorimetric techniques have demonstrated that although binding site 1 (ancillary) has high affinity for metal ion with a binding constant of 2 x 10(-7), binding site 2 (primary) is a low-affinity binding site with a binding constant of 6.3 x 10(-4). These two binding sites act in an independent fashion, and their contribution can be easily dissected by traditional mutational analysis. Our results clearly demonstrate that binding site 1 (ancillary) is the first one to be occupied during metal ion activation, playing a critical role in stabilization of the repressor. In addition, structural data obtained for the mutants Ni-DtxR(H79A,C102D), reported here, and the previously reported DtxR(H79A) have allowed us to propose a mechanism of metal activation for DtxR.


  • Organizational Affiliation
    • Department of Chemistry, Brandeis University, Waltham, MA 02454, USA.

Macromolecule Content 

  • Total Structure Weight: 15.77 kDa 
  • Atom Count: 1,171 
  • Modeled Residue Count: 139 
  • Deposited Residue Count: 139 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Diphtheria toxin repressor mutant139Corynebacterium diphtheriaeMutation(s): 2 
Gene Names: dtxR
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI

Query on NI



Download:Ideal Coordinates CCD File
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.300 (Depositor) 
  • R-Value Work:  0.279 (Depositor) 
  • R-Value Observed: 0.279 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.082α = 90
b = 63.082β = 90
c = 105.987γ = 120
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description