1C8R

BACTERIORHODOPSIN D96N BR STATE AT 2.0 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Observed: 0.126 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.6 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

  • DOI: https://doi.org/10.1126/science.286.5438.255
  • Primary Citation of Related Structures:  
    1C8R, 1C8S

  • 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 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.


  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. hudel@uci.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (BACTERIORHODOPSIN)249Halobacterium salinarumMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LI1
Query on LI1

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL
C42 H86 O3
YERVUJAKCNBGCR-BIHSMRAKSA-N
SQU
Query on SQU

Download Ideal Coordinates CCD File 
O [auth A]2,10,23-TRIMETHYL-TETRACOSANE
C27 H56
ZADHKSJXSZBQFB-HHHXNRCGSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
P [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Observed: 0.126 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.631α = 90
b = 60.631β = 90
c = 108.156γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-12-11
    Changes: Advisory, Derived calculations
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-09
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary