2ZFE

Crystal structure of bacteriorhodopsin-xenon complex

• PDB DOI: https://doi.org/10.2210/pdb2ZFE/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2007-12-31 Released: 2008-11-11 
• Deposition Author(s): Kouyama, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

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: 33.01 kDa 
• Atom Count: 2,099 
• 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	N/A	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
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L3P	D [auth A]	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE C46 H94 O11 P2 TZXJQSKPTCRGCA-VZSPAKCESA-L
L1P	F [auth A], G [auth A], H [auth A]	3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL C43 H89 O6 P UKQGAMWGTOTQPC-ALOLAALWSA-N
L2P	E [auth A]	2,3-DI-PHYTANYL-GLYCEROL C43 H88 O3 ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET	C [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
XE	I [auth A]	XENON Xe FHNFHKCVQCLJFQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.41	α = 90
b = 102.41	β = 90
c = 112.47	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: 2008-11-11 
Deposition Author(s): Kouyama, T.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary