5J7A

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.

Nogly, P.Panneels, V.Nelson, G.Gati, C.Kimura, T.Milne, C.Milathianaki, D.Kubo, M.Wu, W.Conrad, C.Coe, J.Bean, R.Zhao, Y.Bath, P.Dods, R.Harimoorthy, R.Beyerlein, K.R.Rheinberger, J.James, D.DePonte, D.Li, C.Sala, L.Williams, G.J.Hunter, M.S.Koglin, J.E.Berntsen, P.Nango, E.Iwata, S.Chapman, H.N.Fromme, P.Frank, M.Abela, R.Boutet, S.Barty, A.White, T.A.Weierstall, U.Spence, J.Neutze, R.Schertler, G.Standfuss, J.

(2016) Nat Commun 7: 12314-12314

  • DOI: 10.1038/ncomms12314

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proto ...

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.


    Related Citations: 
    • Lipidic cubic phase serial millisecond crystallography using synchrotron radiation.
      Nogly, P.,James, D.,Wang, D.,White, T.A.,Zatsepin, N.,Shilova, A.,Nelson, G.,Liu, H.,Johansson, L.,Heymann, M.,Jaeger, K.,Metz, M.,Wickstrand, C.,Wu, W.,Bath, P.,Berntsen, P.,Oberthuer, D.,Panneels, V.,Cherezov, V.,Chapman, H.,Schertler, G.,Neutze, R.,Spence, J.,Moraes, I.,Burghammer, M.,Standfuss, J.,Weierstall, U.
      (2015) IUCrJ 2: 168


    Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.,SwissFEL, Paul Scherrer Institute, Villigen 5232, Switzerland.,Lawrence Livermore National Laboratory, Livermore 94550, USA.,Biometal Science Laboratory, RIKEN SPring-8 Center, Hyogo 679-5148, Japan.,Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany.,Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA.,Department of Cell Biology, Kyoto University, Kyoto 606-8501, Japan.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Department of Biology, ETH Zurich, Zürich 8093, Switzerland.,Department of Physics, University of Hamburg, 22761 Hamburg, Germany.,PRESTO, JST, Saitama 332-0012, Japan.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,SACLA Science Research Group, RIKEN/SPring-8 Center, Hyogo 679-5148, Japan.,Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin
A
227Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 0 
Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI1
Query on LI1

Download SDF File 
Download CCD File 
A
1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
LIPID FRAGMENT
C42 H86 O3
YERVUJAKCNBGCR-BIHSMRAKSA-N
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 62.000α = 90.00
b = 62.000β = 90.00
c = 110.000γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
PDB_EXTRACTdata extraction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Data collection
  • Version 1.2: 2018-11-14
    Type: Data collection