5J7A

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ncomms12314
  • Primary Citation of Related Structures:  
    5J7A

  • 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 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.


  • Organizational Affiliation

    Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin227Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 62β = 90
c = 110γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Data collection
  • Version 1.2: 2018-11-14
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description