3MBV | pdb_00003mbv

Structure of bacterirhodopsin crystallized in betta-XylOC(16+4) meso phase

• PDB DOI: https://doi.org/10.2210/pdb3MBV/pdb

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


• Deposited: 2010-03-26 Released: 2010-11-03 
• Deposition Author(s): Borshchevskiy, V., Moiseeva, E., Kuklin, A., Bueldt, G., Hato, M., Gordeliy, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.186 (DCC) 

Starting Model: experimental

Literature

Isoprenoid-chained lipid beta-XylOC16+4 A novel molecule for in meso membrane protein crystallization

Borshchevskiy, V., Moiseeva, E., Kuklin, A., Bueldt, G., Hato, M., Gordeliy, V.

(2010) J Cryst Growth 312: 3326-3330

• DOI: https://doi.org/10.1016/j.jcrysgro.2010.08.018

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: 27.53 kDa 
• Atom Count: 1,791 
• Modeled Residue Count: 222 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BXC	C [auth A]	(3R,7R,11R)-3,7,11,15-tetramethylhexadecyl alpha-D-ribopyranoside C25 H50 O5 ZSTFWXWLAGSUTP-RJQIIPCNSA-N
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:  0.203 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.186 (DCC) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.348	α = 90
b = 61.348	β = 90
c = 109.787	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Borshchevskiy, V., Moiseeva, E., Kuklin, A., Bueldt, G., Hato, M., Gordeliy, V.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary