4HE4

Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis.

Pletneva, N.V.Pletnev, V.Z.Souslova, E.Chudakov, D.M.Lukyanov, S.Martynov, V.I.Arhipova, S.Artemyev, I.Wlodawer, A.Dauter, Z.Pletnev, S.

(2013) Acta Crystallogr.,Sect.D 69: 1005-1012

  • DOI: 10.1107/S0907444913004034

  • PubMed Abstract: 
  • The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases ...

    The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow-orange range (535-555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The `yellow' chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.


    Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Yellow fluorescent protein
A, B
246Phialidium sp. SL-2003Mutation(s): 0 
Find proteins for Q6RYS7 (Phialidium sp. SL-2003)
Go to UniProtKB:  Q6RYS7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO
A, B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 102.870α = 90.00
b = 102.870β = 90.00
c = 242.530γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction
SERGUIdata collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references