1AP9 | pdb_00001ap9

X-RAY STRUCTURE OF BACTERIORHODOPSIN FROM MICROCRYSTALS GROWN IN LIPIDIC CUBIC PHASES

• PDB DOI: https://doi.org/10.2210/pdb1AP9/pdb

• Classification: PHOTORECEPTOR
• Organism(s): Halobacterium salinarum
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 1997-07-26 Released: 1998-09-16 
• Deposition Author(s): Pebay-Peyroula, E., Rummel, G., Rosenbusch, J.P., Landau, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.317 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.274 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases.

Pebay-Peyroula, E., Rummel, G., Rosenbusch, J.P., Landau, E.M.

(1997) Science 277: 1676-1681

• PubMed: 9287223 
• DOI: https://doi.org/10.1126/science.277.5332.1676
• Primary Citation Related Structures: 
  1AP9


• PubMed Abstract: 
  

  Lipidic cubic phases provide a continuous three-dimensional bilayer matrix that facilitates nucleation and growth of bacteriorhodopsin microcrystals. The crystals diffract x-rays isotropically to 2.0 angstroms. The structure of this light-driven proton pump was solved at a resolution of 2.5 angstroms by molecular replacement, using previous results from electron crystallographic studies as a model. The earlier structure was generally confirmed, but several differences were found, including loop conformations and side chain residues. Eight water molecules are now identified experimentally in the proton pathway. These findings reveal the constituents of the proton translocation pathway in the ground state.

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Organizational Affiliation: 
• Institut de Biologie Structurale/CEA-CNRS/Université Joseph Fourier, 41 Avenue des Martyrs, F-38027 Grenoble Cedex 1, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 27.1 kDa 
• Atom Count: 1,740 
• Modeled Residue Count: 219 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIORHODOPSIN	A	248	Halobacterium salinarum	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.317 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.274 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.76	α = 90
b = 61.76	β = 90
c = 104.16	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-09-16 
Deposition Author(s): Pebay-Peyroula, E., Rummel, G., Rosenbusch, J.P., Landau, E.M.

Revision History  

• Version 1.0: 1998-09-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary