7SF9 | pdb_00007sf9

Branchiostoma Floridae Violet Fluorescent Protein

• PDB DOI: https://doi.org/10.2210/pdb7SF9/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Branchiostoma floridae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-03 Released: 2022-03-30 
• Deposition Author(s): Pletnev, S., Pletneva, N., Pletnev, V.Z., Muslinkina, L.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.263 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins.

Roldan-Salgado, A., Muslinkina, L., Pletnev, S., Pletneva, N., Pletnev, V., Gaytan, P.

(2022) Protein Sci 31: 688-700

• PubMed: 34936154 
• DOI: https://doi.org/10.1002/pro.4265
• Primary Citation Related Structures: 
  7SF9, 7SFA


• PubMed Abstract: 
  

  We describe an engineered violet fluorescent protein from the lancelet Branchiostoma floridae (bfVFP). This is the first example of a GFP-like fluorescent protein with a stable fluorescent chromophore lacking an imidazolinone ring; instead, it consists of oxidized tyrosine 68 flanked by glycine 67 and alanine 69. bfVFP contains the simplest chromophore reported in fluorescent proteins and was generated from the yellow protein lanFP10A2 by two synergetic mutations, S148H and C166I. The chromophore structure was confirmed crystallographically and by high-resolution mass spectrometry. The photophysical characteristics of bfVFP (323/430 nm, quantum yield 0.33, and E _c 14,300 M ^-1  cm ^-1 ) make it potentially useful for multicolor experiments to expand the excitation range of available FP biomarkers and Förster resonance energy transfer with blue and cyan fluorescent protein acceptors.

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Organizational Affiliation: 
• Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 107.7 kDa 
• Atom Count: 7,559 
• Modeled Residue Count: 883 
• Deposited Residue Count: 952 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Violet Fluorescent Protein	A, B, C, D	238	Branchiostoma floridae	Mutation(s): 0  Gene Names: BRAFLDRAFT_75522
UniProt
Find proteins for C3YRA2 (Branchiostoma floridae) Explore C3YRA2  Go to UniProtKB:  C3YRA2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.263 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.674	α = 90
b = 177.674	β = 90
c = 52.362	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Pletnev, S., Pletneva, N., Pletnev, V.Z., Muslinkina, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description