7OO9 | pdb_00007oo9

Structure of Chloroflexus islandicus LOV domain C85A variant (CisFbFP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

High-resolution structure of a naturally red-shifted LOV domain.

Goncharov, I.M.Smolentseva, A.Semenov, O.Natarov, I.Nazarenko, V.V.Yudenko, A.Remeeva, A.Gushchin, I.

(2021) Biochem Biophys Res Commun 567: 143-147

  • DOI: https://doi.org/10.1016/j.bbrc.2021.06.046
  • Primary Citation Related Structures: 
    7OO9

  • PubMed Abstract: 

    LOV domains are widespread photosensory modules that have also found applications in fluorescence microscopy, optogenetics, and light-driven generation of reactive oxygen species. Many of these applications require stable proteins with altered spectra. Here, we report a flavin-based fluorescent protein CisFbFP derived from Chloroflexus islandicus LOV domain-containing protein. We show that CisFbFP is thermostable, and its absorption and fluorescence spectra are red-shifted for ∼6 nm, which has not been observed for other cysteine-substituted natural LOV domains. We also provide a crystallographic structure of CisFbFP at the resolution of 1.2 Å that reveals alterations in the active site due to replacement of conservative asparagine with a serine. Finally, we discuss the possible effects of presence of cis-proline in the Aβ-Bβ loop on the protein's structure and stability. The findings provide the basis for engineering and color tuning of LOV-based tools for molecular biology.


  • Organizational Affiliation
    • Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.

Macromolecule Content 

  • Total Structure Weight: 26.95 kDa 
  • Atom Count: 2,121 
  • Modeled Residue Count: 212 
  • Deposited Residue Count: 226 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hybrid sensor histidine kinase/response regulator
A, B
113Chloroflexus islandicusMutation(s): 1 
Gene Names: A6A03_05810
EC: 2.7.13.3
UniProt
Find proteins for A0A178LR65 (Chloroflexus islandicus)
Explore A0A178LR65 
Go to UniProtKB:  A0A178LR65
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A178LR65
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.606α = 90
b = 62.541β = 90
c = 64.157γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation21-64-00018

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description