4AS8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Alteration of Fluorescent Protein Spectroscopic Properties Upon Cryoprotection

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

(2012) Acta Crystallogr.,Sect.D 68: 1578

  • DOI: 10.1107/S0907444912037900

  • 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 fluorescen ...

    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.


    Organizational Affiliation

    Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France. vonstett@esrf.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GREEN FLUORESCENT PROTEIN
A
245Aequorea victoriaMutation(s): 7 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRF
Query on CRF
A
L-PEPTIDE LINKINGC17 H18 N4 O4THR, TRP, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.344α = 90.00
b = 62.662β = 90.00
c = 70.205γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Data collection
  • Version 1.3: 2017-12-20
    Type: Database references