4ZF4

Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(Cl1Y), H148D; circular permutant (50-51)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.823 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).

Oltrogge, L.M.Boxer, S.G.

(2015) Acs Cent.Sci. 1: 148-156

  • DOI: 10.1021/acscentsci.5b00160
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to fo ...

    Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy.


    Organizational Affiliation

    Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Green fluorescent protein
A, B
252Aequorea victoriaMutation(s): 18 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4NT
Query on 4NT
A, B
L-peptide linkingC15 H16 Cl N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.823 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.840α = 90.00
b = 68.590β = 100.50
c = 60.880γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM27738

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description