2ZFE

Crystal structure of bacteriorhodopsin-xenon complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin

Hayakawa, N.Kasahara, T.Hasegawa, D.Yoshimura, K.Murakami, M.Kouyama, T.

(2008) J Mol Biol 384: 812-823

  • DOI: https://doi.org/10.1016/j.jmb.2008.09.075
  • Primary Citation of Related Structures:  
    2ZFE

  • PubMed Abstract: 

    To understand the functional role of apolar cavities in bacteriorhodopsin, a light-driven proton pump found in Halobacterium salinarum, we investigated the crystal structure in pressurized xenon or krypton. Diffraction data from the P622 crystal showed that one Xe or Kr atom binds to a preexisting hydrophobic cavity buried between helices C and D, located at the same depth from the membrane surface as Asp96, a key residue in the proton uptake pathway. The occupation fraction of Xe or Kr was calculated as approximately 0.32 at a pressure of 1 MPa. In the unphotolyzed state, the binding of Xe or Kr caused no large deformation of the cavity. However, the proton pumping cycle was greatly perturbed when an aqueous suspension of purple membrane was pressurized with xenon gas; that is, the decay of the M state was accelerated significantly (~5 times at full occupancy), while the decay of an equilibrium state of N and O was slightly decelerated. A similar but much smaller perturbation in the reaction kinetics was observed upon pressurization with krypton gas. In a glycerol/water mixture, xenon-induced acceleration of M decay became less significant in proportion to the water activity. Together with the structure of the xenon-bound protein, these observations suggest that xenon binding helps water molecules permeate into apolar cavities in the proton uptake pathway, thereby accelerating the water-mediated proton transfer from Asp96 to the Schiff base.


  • Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin262N/AMutation(s): 0 
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan:  G37414ZM
GlyCosmos:  G37414ZM
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L3P
Query on L3P

Download Ideal Coordinates CCD File 
D [auth A]2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
L1P
Query on L1P

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL
C43 H89 O6 P
UKQGAMWGTOTQPC-ALOLAALWSA-N
L2P
Query on L2P

Download Ideal Coordinates CCD File 
E [auth A]2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
C [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
XE
Query on XE

Download Ideal Coordinates CCD File 
I [auth A]XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.41α = 90
b = 102.41β = 90
c = 112.47γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2008-11-11 
  • Deposition Author(s): Kouyama, T.

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary