1QM8

Structure of Bacteriorhodopsin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Three-Dimensional Crystal of Bacteriorhodopsin Obtained by Successive Fusion of the Vesicular Assemblies.

Takeda, K.Sato, H.Hino, T.Kono, M.Fukuda, K.Sakurai, I.Okada, T.Kouyama, T.

(1998) J.Mol.Biol. 283: 463

  • DOI: 10.1006/jmbi.1998.2103

  • PubMed Abstract: 
  • When the two-dimensional crystal of bacteriorhodopsin (bR), purple membrane, is incubated at high temperature (32 degreesC) with a small amount of the neutral detergent octylthioglucoside in the presence of the precipitant ammonium sulfate, a large f ...

    When the two-dimensional crystal of bacteriorhodopsin (bR), purple membrane, is incubated at high temperature (32 degreesC) with a small amount of the neutral detergent octylthioglucoside in the presence of the precipitant ammonium sulfate, a large fraction of the membrane fragments is converted into spherical vesicles with a diameter of 50 nm, which are able to assemble into optically isotropic hexagonal crystals when the precipitant concentration is increased. The vesicularization of purple membrane takes place under such a condition that the miscibility of the detergent to the aqueous phase becomes very low, and we suggest that it is initiated by insertion of the detergent molecules into the membrane. At low temperature, the transformation into the vesicular structure is inhibited and no large crystal is produced directly from membrane/detergent/precipitant mixtures. When a suspension of the spherical vesicles produced at the high temperature is cooled and concentrated below 15 degreesC, however, a birefringent hexagonal crystal is produced that diffracts X-rays beyond 2.5 A resolution. This new crystal belongs to the space group P622 with unit cell dimensions of a=b=104.7 A and c=114.1 A, and it is shown to be made up of stacked planar membranes, in each of which the bR trimers are arranged on a honeycomb lattice and the space among the proteins is filled with the detergent molecules and native lipids. These stacked membranes are suggested to be produced by successive fusion of the spherical vesicles. This implies that the crystallization is achieved without any step for complete solubilization of the protein. The present result offers a unique crystallization method that may be applicable to such membrane proteins that are liable to denature in the presence of an excess amount of detergent.


    Related Citations: 
    • Specific Lipid-Protein Interactions in a Novel Honeycomb Lattice Structure of Bacteriorhodopsin
      Sato, H.,Takeda, K.,Tani, K.,Hino, T.,Okada, T.,Nakasako, M.,Kamiya, N.,Kouyama, T.
      (1999) Acta Crystallogr.,Sect.D D55: 1251


    Organizational Affiliation

    Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERIORHODOPSIN
A
248Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L4P
Query on L4P

Download SDF File 
Download CCD File 
A
3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
L1P
Query on L1P

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Download CCD File 
A
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCERO-3-PHOSPHATE
C43 H89 O6 P
UKQGAMWGTOTQPC-ALOLAALWSA-N
 Ligand Interaction
RET
Query on RET

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
GLC
Query on GLC

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A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
L2P
Query on L2P

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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
L3P
Query on L3P

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Download CCD File 
A
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.251 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.100α = 90.00
b = 102.100β = 90.00
c = 112.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance