5BR5

Structure of bacteriorhodopsin crystallized from ND-MSP1E3D1

• PDB DOI: https://doi.org/10.2210/pdb5BR5/pdb

• Classification: ION TRANSPORT
• Organism(s): Halobacterium salinarum
• Expression System: Halobacterium salinarum
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2015-05-29 Released: 2016-09-14 
• Deposition Author(s): Nikolaev, M., Round, E., Gushchin, I., Gordeliy, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Integral Membrane Proteins Can Be Crystallized Directly from Nanodiscs

Nikolaev, M., Round, E., Gushchin, I., Polovinkin, V., Balandin, T., Kuzmichev, P., Shevchenko, V., Borshchevskiy, V., Kuklin, A., Round, A., Bernhard, F., Willbold, D., Buldt, G., Gordeliy, V.

(2017) Cryst Growth Des 17: 945-948

• DOI: https://doi.org/10.1021/acs.cgd.6b01631

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 (software)

Macromolecule Content

• Total Structure Weight: 27.21 kDa 
• Atom Count: 1,749 
• Modelled Residue Count: 222 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	249	Halobacterium salinarum	Mutation(s): 0  Gene Names: bop, VNG_1467G 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: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.98	α = 90
b = 60.98	β = 90
c = 109.99	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Nikolaev, M., Round, E., Gushchin, I., Gordeliy, V.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Structure summary