5BQL | pdb_00005bql

Fluorescent protein cyOFP

• PDB DOI: https://doi.org/10.2210/pdb5BQL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Entacmaea quadricolor
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-29 Released: 2016-06-01 
• Deposition Author(s): Sens, A., Ataie, N., Ng, H.L., Lin, M.Z., Chu, J.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

A Guide to Fluorescent Protein FRET Pairs.

Bajar, B.T., Wang, E.S., Zhang, S., Lin, M.Z., Chu, J.

(2016) Sensors (Basel) 16

• PubMed: 27649177 
• DOI: https://doi.org/10.3390/s16091488
• Primary Citation Related Structures: 
  5BQL


• PubMed Abstract: 
  

  Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies.

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Organizational Affiliation: 
• Medical Scientist Training Program, University of California, Los Angeles, CA 90095, USA. [e-mail].
Harvard College, Cambridge, MA 02138, USA. [e-mail].
Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China. [e-mail].
Departments of Bioengineering and Neurobiology, Stanford University, CA 94305, USA. [e-mail].
Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China. [e-mail].

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: 110 kDa 
• Atom Count: 7,216 
• Modeled Residue Count: 894 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent protein cyOFP	A, B, C, D	242	Entacmaea quadricolor	Mutation(s): 0
UniProt
Find proteins for A0A182DW87 (Escherichia coli) Explore A0A182DW87  Go to UniProtKB:  A0A182DW87

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A, B, C, D	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.124	α = 90
b = 102.764	β = 90
c = 123.254	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Sens, A., Ataie, N., Ng, H.L., Lin, M.Z., Chu, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	1U01NS090600
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P50GM107615

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2018-10-10
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.4: 2019-12-18
  Changes: Author supporting evidence, Structure summary
• Version 1.5: 2025-04-02
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence