6S46

Room temperature structure of the LOV2 domain of phototropin-2 from Arabidopsis thaliana 4158 ms after initiation of illumination, determined with a serial crystallography approach


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron.

Aumonier, S.Santoni, G.Gotthard, G.von Stetten, D.Leonard, G.A.Royant, A.

(2020) IUCrJ 7: 728-736

  • DOI: https://doi.org/10.1107/S2052252520007411
  • Primary Citation of Related Structures:  
    6S45, 6S46

  • PubMed Abstract: 

    The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.


  • Organizational Affiliation

    Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs, Grenoble Cedex 9, 38043, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phototropin-2128Arabidopsis thalianaMutation(s): 0 
Gene Names: PHOT2CAV1KIN7NPL1At5g58140K21L19.6
EC: 2.7.11.1
UniProt
Find proteins for P93025 (Arabidopsis thaliana)
Explore P93025 
Go to UniProtKB:  P93025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93025
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.009α = 90
b = 41.009β = 90
c = 133.152γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description