6OA8 | pdb_00006oa8

Superfolder Green Fluorescent Protein with 4-cyano-L-phenylalanine at the chromophore (position 66)

• PDB DOI: https://doi.org/10.2210/pdb6OA8/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli str. K-12 substr. DH10B
• Mutation(s): No 


• Deposited: 2019-03-15 Released: 2020-08-05 
• Deposition Author(s): Piacentini, J., Olenginski, G.M., Brewer, S.H., Phillips-Piro, C.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein

Olenginski, G.M., Piacentini, J., Harris, D.R., Runko, N., Papoutsis, B.M., Alter, J.R., Hess, K.R., Brewer, S.H., Phillips-Piro, C.M.

(2021) Acta Crystallogr D Biol Crystallogr 

• DOI: https://doi.org/10.1107/S2059798321006525

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.95 kDa 
• Atom Count: 2,442 
• Modeled Residue Count: 233 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A	237	Aequorea victoria	Mutation(s): 0  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
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	M [auth A], N [auth A], O [auth A], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3V	A	L-PEPTIDE LINKING	C16 H16 N4 O4		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.266	α = 90
b = 55.266	β = 90
c = 166.483	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Piacentini, J., Olenginski, G.M., Brewer, S.H., Phillips-Piro, C.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM121984
National Science Foundation (NSF, United States)	United States	CHE-1053946

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 2.0: 2021-07-14
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
• Version 2.1: 2021-08-11
  Changes: Database references
• Version 2.2: 2023-10-11
  Changes: Data collection, Refinement description
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations