Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.80 kDa 
• Atom Count: 2095 
• Residue Count: 227 
• Unique protein chains: 1

1IXF

Crystal Structure of the K intermediate of bacteriorhodopsin

• DOI: 10.2210/pdb1IXF/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Halobacterium salinarum
• Mutation(s): No 


• Deposited: 2002-06-20 Released: 2002-12-18 
• Deposition Author(s): Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.321 
• R-Value Work: 0.291 

Literature

Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin

Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T.

(2002) J Mol Biol 324: 469-481

• PubMed: 12445782 
• DOI: 10.1016/s0022-2836(02)01110-5
• Primary Citation of Related Structures:  
  1IW6, 1IXF


• PubMed Abstract: 
  

Bacteriorhodopsin, the sole membrane protein of the purple membrane of Halobacterium salinarum, functions as a light-driven proton pump. A 3-D crystal of bacteriorhodopsin, which was prepared by the membrane fusion method, was used to investigate structural changes in the primary photoreaction. It was observed that when a frozen crystal was exposed to a low flux of X-ray radiation (5 x 10(14)photons mm(-2)), nearly half of the protein was converted into an orange species, exhibiting absorption peaks at 450 nm, 478 nm and 510 nm. The remainder retained the normal photochemical activity until Asp85 in the active site was decarboxlyated by a higher flux of X-ray radiation (10(16)photons mm(-2)). The procedure of diffraction measurement was improved so as to minimize the effects of the radiation damage and determine the true structural change associated with the primary photoreaction. Our structural model of the K intermediate indicates that the Schiff base linkage and the adjacent bonds in the polyene chain of retinal are largely twisted so that the Schiff base nitrogen atom still interacts with a water molecule located near Asp85. With respect to the other part of the protein, no appreciable displacement is induced in the primary photoreaction.

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Organizational Affiliation: 

Graduate School of Science, Nagoya University, Chikusa, 464-8602, Nagoya, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bacteriorhodopsin	A	248	Halobacterium salinarum	Mutation(s): 0
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	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose	B	3		N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.321 
• R-Value Work: 0.291 
• 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
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-20 
• Released Date: 2002-12-18 
Deposition Author(s): Matsui, Y., Sakai, K., Murakami, M., Shiro, Y., Adachi, S., Okumura, H., Kouyama, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2002-12-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 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