6RBL

TETR(D) E147A MUTANT IN COMPLEX WITH DOXYCYCLINE AND MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding.

Palm, G.J.Buchholz, I.Werten, S.Girbardt, B.Berndt, L.Delcea, M.Hinrichs, W.

(2020) Biochim Biophys Acta Proteins Proteom 1868: 140404-140404

  • DOI: https://doi.org/10.1016/j.bbapap.2020.140404
  • Primary Citation of Related Structures:  
    2XRL, 4B3A, 6FPL, 6FPM, 6FTS, 6QJW, 6QJX, 6RBL, 6RBM, 6RCR, 6RGX

  • PubMed Abstract: 

    Allosteric regulation of the Tet repressor (TetR) homodimer relies on tetracycline binding that abolishes the affinity for the DNA operator. Previously, interpretation of circular dichroism data called for unfolding of the α-helical DNA-binding domains in absence of binding to DNA or tetracycline. Our small angle X-ray scattering of TetR(D) in solution contradicts this unfolding as a physiological process. Instead, in the core domain crystal structures analyses show increased immobilisation of helix α9 and two C-terminal turns of helix α8 upon tetracycline binding. Tetracycline complexes of TetR(D) and four single-site alanine variants were characterised by isothermal titration calorimetry, fluorescence titration, X-ray crystal structures, and melting curves. Five crystal structures confirm that Thr103 is a key residue for the allosteric events of induction, with the T103A variant lacking induction by any tetracycline. The T103A variant shows anti-cooperative inducer binding, and a melting curve of the tetracycline complex different to TetR(D) and other variants. For the N82A variant inducer binding is clearly anti-cooperative but triggers the induced conformation.


  • Organizational Affiliation

    Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489 Greifswald, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetracycline repressor protein class D207Escherichia coliMutation(s): 2 
Gene Names: tetR
UniProt
Find proteins for P0ACT4 (Escherichia coli)
Explore P0ACT4 
Go to UniProtKB:  P0ACT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACT4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DXT (Subject of Investigation/LOI)
Query on DXT

Download Ideal Coordinates CCD File 
B [auth A](4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
C22 H24 N2 O8
JBIWCJUYHHGXTC-AKNGSSGZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 68.3β = 90
c = 179.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary