5EBJ

Joint X-ray/neutron structure of reversibly photoswitching chromogenic protein, Dathail


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.305 

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail.

Langan, P.S.Close, D.W.Coates, L.Rocha, R.C.Ghosh, K.Kiss, C.Waldo, G.Freyer, J.Kovalevsky, A.Bradbury, A.R.

(2016) J Mol Biol 428: 1776-1789

  • DOI: 10.1016/j.jmb.2016.02.029
  • Primary Citation of Related Structures:  
    5EB6, 5EB7, 5EBJ, 5EJU, 5EXU

  • PubMed Abstract: 
  • We report the engineering of a new reversibly switching chromogenic protein, Dathail. Dathail was evolved from the extremely thermostable fluorescent proteins thermal green protein (TGP) and eCGP123 using directed evolution and ratiometric sorting. Dathail has two spectrally distinct chromogenic states with low quantum yields, corresponding to absorbance in a ground state with a maximum at 389nm, and a photo-induced metastable state with a maximum at 497nm ...

    We report the engineering of a new reversibly switching chromogenic protein, Dathail. Dathail was evolved from the extremely thermostable fluorescent proteins thermal green protein (TGP) and eCGP123 using directed evolution and ratiometric sorting. Dathail has two spectrally distinct chromogenic states with low quantum yields, corresponding to absorbance in a ground state with a maximum at 389nm, and a photo-induced metastable state with a maximum at 497nm. In contrast to all previously described photoswitchable proteins, both spectral states of Dathail are non-fluorescent. The photo-induced chromogenic state of Dathail has a lifetime of ~50min at 293K and pH7.5 as measured by UV-Vis spectrophotometry, returning to the ground state through thermal relaxation. X-ray crystallography provided structural insights supporting a change in conformation and coordination in the chromophore pocket as being responsible for Dathail's photoswitching. Neutron crystallography, carried out for the first time on a protein from the green fluorescent protein family, showed a distribution of hydrogen atoms revealing protonation of the chromophore 4-hydroxybenzyl group in the ground state. The neutron structure also supports the hypothesis that the photo-induced proton transfer from the chromophore occurs through water-mediated proton relay into the bulk solvent. Beyond its spectroscopic curiosity, Dathail has several characteristics that are improvements for applications, including low background fluorescence, large spectral separation, rapid switching time, and the ability to switch many times. Therefore, Dathail is likely to be extremely useful in the quickly developing fields of imaging and biosensors, including photochromic Förster resonance energy transfer, high-resolution microscopy, and live tracking within the cell.


    Related Citations: 
    • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
      Adams, P.D., Mustyakimov, M., Afonine, P.V., Langan, P.
      (2009) Acta Crystallogr D Biol Crystallogr D65: 567

    Organizational Affiliation

    Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Electronic address: amb@lanl.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
photoswitching chromogenic proteinA229synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRQ
Query on CRQ
A L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.305 
  • Space Group: P 21 21 2
  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.209α = 90
b = 82.049β = 90
c = 40.889γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Mantiddata reduction
SHELXPREPdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references, Derived calculations, Refinement description