1KME | pdb_00001kme

CRYSTAL STRUCTURE OF BACTERIORHODOPSIN CRYSTALLIZED FROM BICELLES

• PDB DOI: https://doi.org/10.2210/pdb1KME/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Halobacterium salinarum
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2001-12-14 Released: 2002-02-13 
• Deposition Author(s): Faham, S., Bowie, J.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.275 (Depositor) 
• R-Value Work: 
  0.263 (Depositor) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Model: experimental

Literature

Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure.

Faham, S., Bowie, J.U.

(2002) J Mol Biology 316: 1-6

• PubMed: 11829498 
• DOI: https://doi.org/10.1006/jmbi.2001.5295
• Primary Citation Related Structures: 
  1KME


• PubMed Abstract: 
  

  Obtaining crystals of membrane proteins that diffract to high resolution remains a major stumbling block in structure determination. Here we present a new method for crystallizing membrane proteins from a bicelle forming lipid/detergent mixture. The method is flexible and simple to use. As a test case, bacteriorhodopsin (bR) from Halobacterium salinarum was crystallized from a bicellar solution, yielding a new bR crystal form. The crystals belong to space group P2(1) with unit cell dimensions of a=45.0 A, b=108.9 A, c=55.9 A, beta=113.58 degrees and a dimeric asymmetric unit. The structure was solved by molecular replacement and refined at 2.0 A resolution. In all previous bR structures the protein is organized as a parallel trimer, but in the crystals grown from bicelles, the individual bR subunits are arranged in an antiparallel fashion.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1570, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.29 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 454 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A, B	231	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SQU	D [auth A], E [auth A]	2,10,23-TRIMETHYL-TETRACOSANE C27 H56 ZADHKSJXSZBQFB-HHHXNRCGSA-N
RET	C [auth A], H [auth B]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
BGC	F [auth B], G [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.275 (Depositor) 
• R-Value Work:  0.263 (Depositor) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45	α = 90
b = 108.9	β = 113.58
c = 55.9	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-13 
Deposition Author(s): Faham, S., Bowie, J.U.

Revision History  

• Version 1.0: 2002-02-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-20
  Changes: Structure summary