1X0K

Crystal Structure of Bacteriorhodopsin at pH 10

• PDB DOI: https://doi.org/10.2210/pdb1X0K/pdb

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


• Deposited: 2005-03-23 Released: 2005-08-02 
• Deposition Author(s): Okumura, H., Murakami, M., Kouyama, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.309 
• R-Value Work: 0.263 

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: 31.8 kDa 
• Atom Count: 2,088 
• Modelled Residue Count: 227 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A [auth 1]	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose	B [auth A]	3		N/A
Glycosylation Resources
GlyTouCan:  G59827MO GlyCosmos:  G59827MO GlyGen:  G59827MO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L3P	D [auth 1], F [auth 1], G [auth 1], H [auth 1]	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE C46 H94 O11 P2 TZXJQSKPTCRGCA-VZSPAKCESA-L
L2P	E [auth 1]	2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET	C [auth 1]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.309 
• R-Value Work: 0.263 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.45	α = 90
b = 102.45	β = 90
c = 112.81	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Okumura, H., Murakami, M., Kouyama, T.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-04-23
  Changes: Experimental preparation
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary