7R36

Difference-refined structure of fatty acid photodecarboxylase 2 microsecond following 400-nm laser irradiation of the dark-state determined by SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.301 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned.

Hadjidemetriou, K.Coquelle, N.Barends, T.R.M.De Zitter, E.Schlichting, I.Colletier, J.P.Weik, M.

(2022) Acta Crystallogr D Struct Biol 78: 1131-1142

  • DOI: https://doi.org/10.1107/S2059798322007525
  • Primary Citation of Related Structures:  
    7R33, 7R34, 7R35, 7R36

  • PubMed Abstract: 

    Upon absorption of a blue-light photon, fatty-acid photodecarboxylase catalyzes the decarboxylation of free fatty acids to form hydrocarbons (for example alkanes or alkenes). The major components of the catalytic mechanism have recently been elucidated by combining static and time-resolved serial femtosecond crystallography (TR-SFX), time-resolved vibrational and electronic spectroscopies, quantum-chemical calculations and site-directed mutagenesis [Sorigué et al. (2021), Science, 372, eabd5687]. The TR-SFX experiments, which were carried out at four different picosecond to microsecond pump-probe delays, yielded input for the calculation of Fourier difference maps that demonstrated light-induced decarboxylation. Here, some of the difficulties encountered during the experiment as well as during data processing are highlighted, in particular regarding space-group assignment, a pump-laser power titration is described and data analysis is extended by structure-factor extrapolation of the TR-SFX data. Structure refinement against extrapolated structure factors reveals a reorientation of the generated hydrocarbon and the formation of a photoproduct close to Cys432 and Arg451. Identification of its chemical nature, CO 2 or bicarbonate, was not possible because of the limited data quality, which was assigned to specificities of the crystalline system. Further TR-SFX experiments on a different crystal form are required to identify the photoproducts and their movements during the catalytic cycle.


  • Organizational Affiliation

    Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid photodecarboxylase, chloroplastic
A, B
578Chlorella variabilisMutation(s): 0 
Gene Names: FAPCHLNCDRAFT_28598
EC: 4.1.1.106
UniProt
Find proteins for A0A248QE08 (Chlorella variabilis)
Explore A0A248QE08 
Go to UniProtKB:  A0A248QE08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A248QE08
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.301 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.39α = 90
b = 60.01β = 90.6
c = 182.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description