7YEU

Superfolder green fluorescent protein with phosphine unnatural amino acid P3BF

• PDB DOI: https://doi.org/10.2210/pdb7YEU/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-06 Released: 2023-07-26 
• Deposition Author(s): Hu, C., Duan, H.Z., Liu, X.H., Chen, Y.X., Wang, J.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.191 
• R-Value Work: 0.160 

Literature

Genetically Encoded Phosphine Ligand for Metalloprotein Design.

Duan, H.Z., Hu, C., Li, Y.L., Wang, S.H., Xia, Y., Liu, X., Wang, J., Chen, Y.X.

(2022) J Am Chem Soc 144: 22831-22837

• PubMed: 36417425 
• DOI: https://doi.org/10.1021/jacs.2c09683
• Primary Citation of Related Structures:  
  7YEU


• PubMed Abstract: 
  

  Phosphine ligands are the most important class of ligands for cross-coupling reactions due to their unique electronic and steric properties. However, metalloproteins generally rely on nitrogen, sulfur, or oxygen ligands. Here, we report the genetic incorporation of P3BF, which contains a biocompatible borane-protected phosphine, into proteins. This step is followed by a straightforward one-pot strategy to perform deboronation and palladium coordination in aqueous and aerobic conditions. The genetically encoded phosphine ligand P3BF should significantly expand our ability to design functional metalloproteins.

---

Organizational Affiliation: 

Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P.R. China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 27.37 kDa 
• Atom Count: 2,357 
• Modelled Residue Count: 237 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superfolder green fluorescent protein	A	240	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GYS	A	L-PEPTIDE LINKING	C14 H15 N3 O5		SER, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.191 
• R-Value Work: 0.160 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.603	α = 90
b = 87.603	β = 90
c = 114.571	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Hu, C., Duan, H.Z., Liu, X.H., Chen, Y.X., Wang, J.Y.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177059
Ministry of Science and Technology (MoST, China)	China	2021YFC2103900
Ministry of Science and Technology (MoST, China)	China	2018YFA0507600

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-02-28
  Changes: Database references, Structure summary