1C8S

BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution.

Luecke, H.Schobert, B.Richter, H.T.Cartailler, J.P.Lanyi, J.K.

(1999) Science 286: 255-260

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The tr ...

    Crystal structures of the Asp96 to Asn mutant of the light-driven proton pump bacteriorhodopsin and its M photointermediate produced by illumination at ambient temperature have been determined to 1.8 and 2.0 angstroms resolution, respectively. The trapped photoproduct corresponds to the late M state in the transport cycle-that is, after proton transfer to Asp85 and release of a proton to the extracellular membrane surface, but before reprotonation of the deprotonated retinal Schiff base. Its density map describes displacements of side chains near the retinal induced by its photoisomerization to 13-cis,15-anti and an extensive rearrangement of the three-dimensional network of hydrogen-bonded residues and bound water that accounts for the changed pKa values (where Ka is the acid constant) of the Schiff base and Asp85. The structural changes detected suggest the means for conserving energy at the active site and for ensuring the directionality of proton translocation.


    Related Citations: 
    • Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution
      Luecke, H.,Schobert, B.,Richter, H.-T.,Cartailler, J.-P.,Lanyi, J.K.
      (1999) J.Mol.Biol. 291: 899
    • Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution
      Luecke, H.,Richter, H.-T.,Lanyi, J.K.
      (1998) Science 280: 1934


    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 ("M" STATE INTERMEDIATE)
A
196Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 1 
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 3 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
SQU
Query on SQU

Download SDF File 
Download CCD File 
A
2,10,23-TRIMETHYL-TETRACOSANE
LIPID FRAGMENT
C27 H56
ZADHKSJXSZBQFB-HHHXNRCGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 60.631α = 90.00
b = 60.631β = 90.00
c = 108.156γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-07-29 
  • Released Date: 1999-10-20 
  • Deposition Author(s): Luecke, H.

Revision History 

  • Version 1.0: 1999-10-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance