3V3D

Crystal Structure of an eYFP single mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Improving the second-order nonlinear optical response of fluorescent proteins: the symmetry argument.

De Meulenaere, E.Nguyen Bich, N.de Wergifosse, M.Van Hecke, K.Van Meervelt, L.Vanderleyden, J.Champagne, B.Clays, K.

(2013) J.Am.Chem.Soc. 135: 4061-4069

  • DOI: 10.1021/ja400098b

  • PubMed Abstract: 
  • We have successfully designed and expressed a new fluorescent protein with improved second-order nonlinear optical properties. It is the first time that a fluorescent protein has been rationally altered for this particular characteristic. On the basi ...

    We have successfully designed and expressed a new fluorescent protein with improved second-order nonlinear optical properties. It is the first time that a fluorescent protein has been rationally altered for this particular characteristic. On the basis of the specific noncentrosymmetry requirements for second-order nonlinear optical effects, we had hypothesized that the surprisingly low first hyperpolarizability (β) of the enhanced yellow fluorescent protein (eYFP) could be explained by centrosymmetric stacking of the chromophoric Tyr66 and the neighboring Tyr203 residue. The inversion center was removed by mutating Tyr203 into Phe203, with minor changes in the linear optical properties and even an improved fluorescence quantum yield. Structure determination by X-ray crystallography as well as linear optical characterization corroborate a correct folding and maturation. Measurement of β by means of hyper-Rayleigh scattering (HRS) as well as their analysis using quantum chemistry calculations validate our hypothesis. This observation can eventually lead to improved red fluorescent proteins for even better performance. On the basis of the specific function (second-harmonic generation), the color of its emission, and in analogy with the "fruit" names, we propose SHardonnay as the name for this Tyr203Phe mutant of eYFP.


    Organizational Affiliation

    Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, BE-3001 Leuven, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Yellow fluorescent protein
A
259Aequorea victoriaMutation(s): 4 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.858α = 90.00
b = 59.858β = 90.00
c = 165.540γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references
  • Version 1.2: 2013-03-27
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description