4J88

Dark-state structure of sfGFP containing the unnatural amino acid p-azido-phenylalanine at residue 66

• PDB DOI: https://doi.org/10.2210/pdb4J88/pdb

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


• Deposited: 2013-02-14 Released: 2013-06-26 
• Deposition Author(s): Reddington, S.C., Jones, D.D., Rizkallah, P.J., Tippmann, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.228 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Different Photochemical Events of a Genetically Encoded Phenyl Azide Define and Modulate GFP Fluorescence.

Reddington, S.C., Rizkallah, P.J., Watson, P.D., Pearson, R., Tippmann, E.M., Jones, D.D.

(2013) Angew Chem Int Ed Engl 52: 5974-5977

• PubMed: 23620472 
• DOI: https://doi.org/10.1002/anie.201301490
• Primary Citation of Related Structures:  
  4J88, 4J89, 4J8A


• PubMed Abstract: 
  

  Expanding the genetic code opens new avenues to modulate protein function in real time. By genetically incorporating photoreactive phenyl azide, the fluorescent properties of green fluorescent protein (GFP) can be modulated by light. Depending on the residue in GFP programmed to incorporate the phenyl azide, different effects on function and photochemical pathways are observed.

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Organizational Affiliation: 

School of Biosciences, Cardiff University, Cardiff, UK.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 58.51 kDa 
• Atom Count: 4,141 
• Modelled Residue Count: 455 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	245	Aequorea victoria	Mutation(s): 10  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	AA [auth A], BA [auth A], Z [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], GA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CQ1	A, B	PEPTIDE LINKING	C15 H16 N6 O4		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.228 
• R-Value Work: 0.165 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.43	α = 90
b = 97.56	β = 90
c = 102.9	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Reddington, S.C., Jones, D.D., Rizkallah, P.J., Tippmann, E.M.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations