1BRX

BACTERIORHODOPSIN/LIPID COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.298 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution.

Luecke, H.Richter, H.T.Lanyi, J.K.

(1998) Science 280: 1934-1937


  • PubMed Abstract: 
  • Photoisomerization of the retinal of bacteriorhodopsin initiates a cyclic reaction in which a proton is translocated across the membrane. Studies of this protein promise a better understanding of how ion pumps function. Together with a large amount o ...

    Photoisomerization of the retinal of bacteriorhodopsin initiates a cyclic reaction in which a proton is translocated across the membrane. Studies of this protein promise a better understanding of how ion pumps function. Together with a large amount of spectroscopic and mutational data, the atomic structure of bacteriorhodopsin, determined in the last decade at increasing resolutions, has suggested plausible but often contradictory mechanisms. X-ray diffraction of bacteriorhodopsin crystals grown in cubic lipid phase revealed unexpected two-fold symmetries that indicate merohedral twinning along the crystallographic c axis. The structure, refined to 2.3 angstroms taking this twinning into account, is different from earlier models, including that most recently reported. One of the carboxyl oxygen atoms of the proton acceptor Asp85 is connected to the proton donor, the retinal Schiff base, through a hydrogen-bonded water and forms a second hydrogen bond with another water. The other carboxyl oxygen atom of Asp85 accepts a hydrogen bond from Thr89. This structure forms the active site. The nearby Arg82 is the center of a network of numerous hydrogen-bonded residues and an ordered water molecule. This network defines the pathway of the proton from the buried Schiff base to the extracellular surface.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. HUDEL@UCI.EDU




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERIORHODOPSIN
A
248Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 0 
Gene Names: bop
Membrane protein
mpstruct
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.298 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 60.850α = 90.00
b = 60.850β = 90.00
c = 108.400γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
HKLdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance