5OQE

XFEL structure of the on state of a reversibly photoswitching fluorescent protein determined using the droplet injection method


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

X-ray Free Electron Laser Determination of Crystal Structures of Dark and Light States of a Reversibly Photoswitching Fluorescent Protein at Room Temperature.

Hutchison, C.D.M.Cordon-Preciado, V.Morgan, R.M.L.Nakane, T.Ferreira, J.Dorlhiac, G.Sanchez-Gonzalez, A.Johnson, A.S.Fitzpatrick, A.Fare, C.Marangos, J.P.Yoon, C.H.Hunter, M.S.DePonte, D.P.Boutet, S.Owada, S.Tanaka, R.Tono, K.Iwata, S.van Thor, J.J.

(2017) Int J Mol Sci 18

  • DOI: https://doi.org/10.3390/ijms18091918
  • Primary Citation of Related Structures:  
    5OOZ, 5OQ9, 5OQA, 5OQE

  • PubMed Abstract: 

    The photochromic fluorescent protein Skylan-NS (Nonlinear Structured illumination variant mEos3.1H62L) is a reversibly photoswitchable fluorescent protein which has an unilluminated/ground state with an anionic and cis chromophore conformation and high fluorescence quantum yield. Photo-conversion with illumination at 515 nm generates a meta-stable intermediate with neutral trans-chromophore structure that has a 4 h lifetime. We present X-ray crystal structures of the cis (on) state at 1.9 Angstrom resolution and the trans (off) state at a limiting resolution of 1.55 Angstrom from serial femtosecond crystallography experiments conducted at SPring-8 Angstrom Compact Free Electron Laser (SACLA) at 7.0 keV and 10.5 keV, and at Linac Coherent Light Source (LCLS) at 9.5 keV. We present a comparison of the data reduction and structure determination statistics for the two facilities which differ in flux, beam characteristics and detector technologies. Furthermore, a comparison of droplet on demand, grease injection and Gas Dynamic Virtual Nozzle (GDVN) injection shows no significant differences in limiting resolution. The photoconversion of the on- to the off-state includes both internal and surface exposed protein structural changes, occurring in regions that lack crystal contacts in the orthorhombic crystal form.


  • Organizational Affiliation

    Molecular Biophysics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. christopher.hutchison05@imperial.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Green to red photoconvertible GFP-like protein EosFP223Lobophyllia hemprichiiMutation(s): 10 
UniProt
Find proteins for Q5S6Z9 (Lobophyllia hemprichii)
Explore Q5S6Z9 
Go to UniProtKB:  Q5S6Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S6Z9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
VYA
Query on VYA
A
L-PEPTIDE LINKINGC17 H21 N3 O4LEU, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.8α = 90
b = 74.6β = 90
c = 79.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations