7XJC

Crystal structure of bacteriorhodopsin in the ground and K states after green laser irradiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.131 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin

Taguchi, S.Niwa, S.Dao, H.A.Tanaka, Y.Takeda, R.Fukai, S.Hasegawa, K.Takeda, K.

(2023) Commun Biol 6: 190


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin230Halobacterium salinarum NRC-1Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2P
Query on L2P

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
SQU
Query on SQU

Download Ideal Coordinates CCD File 
H [auth A],
R [auth A],
S [auth A],
T [auth A]
2,10,23-TRIMETHYL-TETRACOSANE
C27 H56
ZADHKSJXSZBQFB-HHHXNRCGSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.131 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.57α = 90
b = 60.57β = 90
c = 110.89γ = 120
Software Package:
Software NamePurpose
SHELXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary