6RHF

Structure of Chloroflexus aggregans Cagg_3753 LOV domain C85A variant (CagFbFP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies.

Nazarenko, V.V.Remeeva, A.Yudenko, A.Kovalev, K.Dubenko, A.Goncharov, I.M.Kuzmichev, P.Rogachev, A.V.Buslaev, P.Borshchevskiy, V.Mishin, A.Dhoke, G.V.Schwaneberg, U.Davari, M.D.Jaeger, K.E.Krauss, U.Gordeliy, V.Gushchin, I.

(2019) Photochem. Photobiol. Sci. --: --

  • DOI: 10.1039/c9pp00067d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Light-Oxygen-Voltage (LOV) domains are conserved parts of photoreceptors in plants, bacteria and fungi that bind flavins as chromophores and detect blue light. In the past, LOV domain variants have been developed as fluorescent reporter proteins (cal ...

    Light-Oxygen-Voltage (LOV) domains are conserved parts of photoreceptors in plants, bacteria and fungi that bind flavins as chromophores and detect blue light. In the past, LOV domain variants have been developed as fluorescent reporter proteins (called flavin-based fluorescent proteins; FbFPs), which due to their ability to fluoresce under anaerobic conditions, fast folding kinetics and a small size of ∼12-16 kDa are a promising reporter system for quantitative real-time analysis of biological processes. Here, we present a small thermostable flavin-based fluorescent protein CagFbFP derived from a soluble LOV domain-containing histidine kinase from the thermophilic bacterium Chloroflexus aggregans. CagFbFP is composed of 107 amino acids with a molecular weight of 11.6 kDa and consists only of the conserved LOV core domain. The protein is thermostable with a melting point of about 68 °C. It crystallizes easily and its crystals diffract to 1.07 Å. Both the crystal structure and small angle scattering data show that the protein is a dimer. Unexpectedly, glutamine 148, which in LOV photoreceptor proteins is the key residue responsible for signal transduction, occupies two conformations. Molecular dynamics simulations show that the two conformations interconvert rapidly. The crystal structure of the wild-type Chloroflexus aggregans LOV domain determined at 1.22 Å resolution confirmed the presence of two alternative conformations of the glutamine 148 side chain. Overall, this protein, due to its stability and ease of crystallization, appears to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.


    Organizational Affiliation

    Moscow Institute of Physics and Technology, Dolgoprudny, Russia. ivan.gushchin@phystech.edu and Joint Institute for Nuclear Research, Dubna, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. ivan.gushchin@phystech.edu.,Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany and IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. ivan.gushchin@phystech.edu and ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany and Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany and DWI-Leibniz Institut für Interaktive Materialien, Aachen, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. ivan.gushchin@phystech.edu and ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany and Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France and Institute of Crystallography, RWTH Aachen University, Aachen, Germany.,Institute of Biotechnology, RWTH Aachen University, Aachen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Multi-sensor hybrid histidine kinase
A, B
113Chloroflexus aggregans (strain MD-66 / DSM 9485)Mutation(s): 0 
Find proteins for B8GAY9 (Chloroflexus aggregans (strain MD-66 / DSM 9485))
Go to UniProtKB:  B8GAY9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.934α = 90.00
b = 110.044β = 90.00
c = 38.945γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic Research18-34-00742

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references