4X32

Bacteriorhodopsin ground state structure collected in cryo conditions from crystals obtained in LCP with PEG as a precipitant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 168-176

  • DOI: 10.1107/S2052252514026487
  • Primary Citation of Related Structures:  
  • Also Cited By: 5J7A

  • PubMed Abstract: 
  • Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electr ...

    Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway.


    Organizational Affiliation

    European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France.,Department of Physics, Arizona State University, Tempe, AZ 85287, USA.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany ; Department of Physics, University of Hamburg, Hamburg 22607, Germany.,European Synchrotron Radiation Facility, Grenoble Cedex 9, F-38043, France ; Department of Analytical Chemistry, Ghent University, Ghent B-9000, Belgium.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California USA.,Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland ; Deparment of Biology, ETH Zurich, Zürich 8093, Switzerland.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Oxfordshire OX11 0DE, England ; Department of Life Sciences, Imperial College London, London, England ; Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Didcot, Oxfordshire OX11 0FA, England.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany ; Centre for Ultrafast Imaging, Hamburg 22607, Germany.,Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin
A
228Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 0 
Gene Names: bop
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Bacteriorhodopsin (BR)
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: 1.9 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.172 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 60.525α = 90.00
b = 60.525β = 90.00
c = 101.480γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Database references