1XQM | pdb_00001xqm

Variations on the GFP chromophore scaffold: A fragmented 5-membered heterocycle revealed in the 2.1A crystal structure of a non-fluorescent chromoprotein

• PDB DOI: https://doi.org/10.2210/pdb1XQM/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Anemonia sulcata
• Mutation(s): Yes 


• Deposited: 2004-10-13 Released: 2004-11-16 
• Deposition Author(s): Wilmann, P.G., Petersen, J., Devenish, R.J., Prescott, M., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata

Wilmann, P.G., Petersen, J., Devenish, R.J., Prescott, M., Rossjohn, J.

(2005) J Biological Chem 280: 2401-2404

• PubMed: 15542608 
• DOI: https://doi.org/10.1074/jbc.C400484200
• Primary Citation Related Structures: 
  1XQM


• PubMed Abstract: 
  

  We have determined to 2.1 A resolution the crystal structure of a dark state, kindling fluorescent protein isolated from the sea anemone, Anemonia sulcata. The chromophore sequence Met(63)-Tyr(64)-Gly(65) of the A. sulcata chromoprotein was previously proposed to comprise a 6-membered pyrazine-type heterocycle (Martynov, V. I., Savitsky, A. P., Martynova, N. Y., Savitsky, P. A., Lukyanov, K. A., and Lukyanov, S. A. (2001) J. Biol. Chem. 276, 21012-21016). However, our crystallographic data revealed the chromophore to comprise a 5-membered p-hydroxybenzylideneimidazolinone moiety that adopts a non-coplanar trans conformation within the interior of the GFP beta-can fold. Unexpectedly, fragmentation of the polypeptide was found to occur within the chromophore moiety, at the bond between Cys(62C) and Met(63N1.) Our structural data reveal that fragmentation of the chromophore represents an intrinsic, autocatalytic step toward the formation of the mature chromophore within the specific GFP-like proteins.

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Organizational Affiliation: 
• Protein Crystallography Unit, Monash Centre for Synchrotron Science.

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 PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 25.9 kDa 
• Atom Count: 1,924 
• Modeled Residue Count: 228 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
kindling fluorescent protein	A	230	N/A	Mutation(s): 1
UniProt
Find proteins for Q9GZ28 (Anemonia sulcata) Explore Q9GZ28  Go to UniProtKB:  Q9GZ28

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CH6	A	L-PEPTIDE LINKING	C16 H19 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.482	α = 90
b = 112.482	β = 90
c = 96.906	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-16 
Deposition Author(s): Wilmann, P.G., Petersen, J., Devenish, R.J., Prescott, M., Rossjohn, J.

Revision History  

• Version 1.0: 2004-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-09
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence