5YR3 | pdb_00005yr3

Structure of sfYFP66BPA

• PDB DOI: https://doi.org/10.2210/pdb5YR3/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2017-11-08 Released: 2019-01-30 
• Deposition Author(s): Kang, F., Wang, L., Wang, J.
• Funding Organization(s): Ministry of Science and Technology (China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

sfYFP66BPA

Kang, F., Wang, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 25.43 kDa 
• Atom Count: 1,904 
• Modeled Residue Count: 225 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Yellow fluorescent protein	A	225	Aequorea victoria	Mutation(s): 14  Gene Names: yfp
UniProt
Find proteins for A0A059PIR9 (Aequorea victoria) Explore A0A059PIR9  Go to UniProtKB:  A0A059PIR9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BF6	A	L-PEPTIDE LINKING	C20 H17 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.713	α = 90
b = 51.713	β = 90
c = 178.977	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: 2019-01-30 
Deposition Author(s): Kang, F., Wang, L., Wang, J.

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2017YFA0503704

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description