4AS8 | pdb_00004as8

X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene glycol

• PDB DOI: https://doi.org/10.2210/pdb4AS8/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-04-29 Released: 2012-10-31 
• Deposition Author(s): von Stetten, D., Batot, G., Noirclerc-Savoye, M., Royant, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.132 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Alteration of Fluorescent Protein Spectroscopic Properties Upon Cryoprotection

von Stetten, D., Batot, G., Noirclerc-Savoye, M., Royant, A.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1578

• PubMed: 23090407 
• DOI: https://doi.org/10.1107/S0907444912037900
• Primary Citation Related Structures: 
  4AS8


• PubMed Abstract: 
  

  Cryoprotection of a protein crystal by addition of small-molecule compounds may sometimes affect the structure of its active site. The spectroscopic and structural effects of the two cryoprotectants glycerol and ethylene glycol on the cyan fluorescent protein Cerulean were investigated. While glycerol had almost no noticeable effect, ethylene glycol was shown to induce a systematic red shift of the UV-vis absorption and fluorescence emission spectra. Additionally, ethylene glycol molecules were shown to enter the core of the protein, with one of them binding in close vicinity to the chromophore, which provides a sound explanation for the observed spectroscopic changes. These results highlight the need to systematically record spectroscopic data on crystals of light-absorbing proteins and reinforce the notion that fluorescent proteins must not been seen as rigid structures.

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Organizational Affiliation: 
• Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 28.33 kDa 
• Atom Count: 2,303 
• Modeled Residue Count: 229 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GREEN FLUORESCENT PROTEIN	A	243	Aequorea victoria	Mutation(s): 8
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRF	A	L-PEPTIDE LINKING	C17 H18 N4 O4		THR, TRP, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.132 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.344	α = 90
b = 62.662	β = 90
c = 70.205	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): von Stetten, D., Batot, G., Noirclerc-Savoye, M., Royant, A.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 1.3: 2017-12-20
  Changes: Database references
• Version 1.4: 2019-10-23
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-13
  Changes: Structure summary