3VI0

Crystal structure of the O intermediate of the L93A mutant of bacteriorhodopsin

• PDB DOI: https://doi.org/10.2210/pdb3VI0/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum NRC-1
• Expression System: Halobacterium
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2011-09-13 Released: 2012-06-13 
• Deposition Author(s): Kouyama, T., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.348 
• R-Value Work: 0.288 
• R-Value Observed: 0.288 

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: 30.06 kDa 
• Atom Count: 1,905 
• Modelled Residue Count: 227 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	262	Halobacterium salinarum NRC-1	Mutation(s): 1  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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3-O-sulfo-beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G37414ZM GlyCosmos:  G37414ZM

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L2P	E [auth A]	2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-N
SOG	D [auth A]	octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N
RET	C [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.348 
• R-Value Work: 0.288 
• R-Value Observed: 0.288 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.3	α = 90
b = 102.3	β = 90
c = 112.3	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Kouyama, T., Zhang, J.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary