8B6R

X-ray structure of the haloalkane dehalogenase HaloTag7 labeled with a chloroalkane Cyanine3 fluorophore substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A general method for the development of multicolor biosensors with large dynamic ranges.

Hellweg, L.Edenhofer, A.Barck, L.Huppertz, M.C.Frei, M.S.Tarnawski, M.Bergner, A.Koch, B.Johnsson, K.Hiblot, J.

(2023) Nat Chem Biol 19: 1147-1157

  • DOI: https://doi.org/10.1038/s41589-023-01350-1
  • Primary Citation of Related Structures:  
    8B6R, 8B6S, 8B6T

  • PubMed Abstract: 

    Fluorescent biosensors enable the study of cell physiology with spatiotemporal resolution; yet, most biosensors suffer from relatively low dynamic ranges. Here, we introduce a family of designed Förster resonance energy transfer (FRET) pairs with near-quantitative FRET efficiencies based on the reversible interaction of fluorescent proteins with a fluorescently labeled HaloTag. These FRET pairs enabled the straightforward design of biosensors for calcium, ATP and NAD + with unprecedented dynamic ranges. The color of each of these biosensors can be readily tuned by changing either the fluorescent protein or the synthetic fluorophore, which enables simultaneous monitoring of free NAD + in different subcellular compartments following genotoxic stress. Minimal modifications of these biosensors furthermore allow their readout to be switched to fluorescence intensity, fluorescence lifetime or bioluminescence. These FRET pairs thus establish a new concept for the development of highly sensitive and tunable biosensors.


  • Organizational Affiliation

    Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase293Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 21 
Gene Names: dhaA
EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp)
Explore P0A3G3 
Go to UniProtKB:  P0A3G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PJI (Subject of Investigation/LOI)
Query on PJI

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[2-[2-(6-chloranylhexoxy)ethoxy]ethyl]-6-[3,3-dimethyl-2-[(~{E})-3-(1,3,3-trimethylindol-2-ylidene)prop-1-enyl]indol-1-ium-1-yl]hexanamide
C40 H57 Cl N3 O3
PMDIAZIQXAWRGJ-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.56α = 90
b = 112.56β = 90
c = 44.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references