4AS8

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.132
R-Value Work: 0.116
R-Value Observed: 0.117

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 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 D Biol Crystallogr 68: 1578

PubMed: 23090407 Search on PubMed
DOI: https://doi.org/10.1107/S0907444912037900
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRF Query on 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
R-Value Work: 0.116
R-Value Observed: 0.117
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-10-31

Deposition Author(s):

Revision History (Full details and data files)

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