5ZIN

Crystal structure of bacteriorhodopsin at 1.27 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray structure analysis of bacteriorhodopsin at 1.3 angstrom resolution.

Hasegawa, N.Jonotsuka, H.Miki, K.Takeda, K.

(2018) Sci Rep 8: 13123-13123

  • DOI: 10.1038/s41598-018-31370-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacteriorhodopsin (bR) of Halobacterium salinarum is a membrane protein that acts as a light-driven proton pump. bR and its homologues have recently been utilized in optogenetics and other applications. Although the structures of those have been repo ...

    Bacteriorhodopsin (bR) of Halobacterium salinarum is a membrane protein that acts as a light-driven proton pump. bR and its homologues have recently been utilized in optogenetics and other applications. Although the structures of those have been reported so far, the resolutions are not sufficient for elucidation of the intrinsic structural features critical to the color tuning and ion pumping properties. Here we report the accurate crystallographic analysis of bR in the ground state. The influence of X-rays was suppressed by collecting the data under a low irradiation dose at 15 K. Consequently, individual atoms could be separately observed in the electron density map at better than 1.3 Å resolution. Residues from Thr5 to Ala233 were continuously constructed in the model. The twist of the retinal polyene was determined to be different from those in the previous models. Two conformations were observed for the proton release region. We discuss the meaning of these fine structural features.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. ktakeda@kuchem.kyoto-u.ac.jp.




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
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
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
L2P
Query on L2P

Download SDF File 
Download CCD File 
A
2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.130 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 60.630α = 90.00
b = 60.630β = 90.00
c = 110.640γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SHELXLrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan25440020, 17H03643

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release