1HCJ

Photoproduct of the wild-type Aequorea victoria Green Fluorescent Protein

• PDB DOI: https://doi.org/10.2210/pdb1HCJ/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli M15
• Mutation(s): Yes 


• Deposited: 2001-05-04 Released: 2001-12-07 
• Deposition Author(s): Van Thor, J.J., Gensch, T., Hellingwerf, K.J., Johnson, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 

Starting Model: experimental

Literature

Phototransformation of Green Fluorescent Protein with Uv and Visible Light Leads to Decarboxylation of Glutamate 222

Van Thor, J.J., Gensch, T., Hellingwerf, K.J., Johnson, L.

(2002) Nat Struct Biol 9: 37

• PubMed: 11740505 
• DOI: https://doi.org/10.1038/nsb739
• Primary Citation of Related Structures:  
  1HCJ


• PubMed Abstract: 
  

  Wild type green fluorescent protein (GFP) from Aequorea victoria absorbs predominantly at 398 nm. Illumination with UV (254 nm) or visible (390 nm) light transforms this state (GFP(398)) into one absorbing at 483 nm (GFP(483)). Here we show that this photoconversion of GFP is a one-photon process that is paralleled by decarboxylation of Glu 222. We propose a mechanism in which decarboxylation is due to electron transfer between the gamma-carboxylate of Glu 222 and the p-hydroxybenzylidene-imidazolidinone chromophore of GFP, followed by reverse transfer of an electron and a proton to the remaining carbon side chain atom of Glu 222. Oxidative decarboxylation of a gamma-carboxylate represents a new type of posttranslational modification that may also occur in enzymes with high-potential reaction intermediates.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 107.55 kDa 
• Atom Count: 7,879 
• Modelled Residue Count: 909 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GREEN FLUORESCENT PROTEIN	A, B, C, D	236	Aequorea victoria	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A, B, C, D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
GYS	A, B, C, D	L-PEPTIDE LINKING	C14 H15 N3 O5		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.209 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.77	α = 90
b = 65.67	β = 103.88
c = 110.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-07 
Deposition Author(s): Van Thor, J.J., Gensch, T., Hellingwerf, K.J., Johnson, L.

Revision History  

• Version 1.0: 2001-12-07
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2019-05-15
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-10-23
  Changes: Data collection, Database references, Other
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2023-12-13
  Changes: Refinement description