The green fluorescent protein WasCFP with a tryptophan-based chromophore (Thr65-Trp66- Gly67) exhibits considerable pH-dependent changes of spectral properties related to the reversible processes of tryptophan ionization and protonation. The crystal structure of WasCFP at pH 10.0, 8.0, and 5.5 was determined in our earlier studies. The spatial structure of WasCFP at an extremely low pH of 2.0 has been determined by X-ray diffraction with a resolution of 1.3 Å in the present study. Synchronous changes in the conformation of amino acid residue side chains in the environment of the chromophore and the related changes in the local hydrogen bond network involving the chromophore were shown to occur at sequential pH changes from 10.0 to 2.0. A quantum chemical study of the effect of interactions between the chromophore and the key amino acid residues from its immediate environment has been performed.