Crystal structure of Green Fluorescent Protein (GFP); S65T, Y66(Cl2Y), H148D; circular permutant ( 50-51)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


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: https://doi.org/10.1021/acscentsci.5b00160
  • Primary Citation of Related Structures:  
    4ZF3, 4ZF4, 4ZF5

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein
A, B
252Aequorea victoriaMutation(s): 19 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42212
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on 4NU
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.14α = 90
b = 68.13β = 102.33
c = 58γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM27738

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2017-09-27
    Changes: Data collection
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection, Derived calculations