3WQJ

Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of archaerhodopsin-2 at 1.8 A resolution

Kouyama, T.Fujii, R.Kanada, S.Nakanishi, T.Chan, S.K.Murakami, M.

(2014) Acta Crystallogr.,Sect.D 70: 2692-2701


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Archaerhodopsin-2
A
259Halobacterium sp. (strain aus-2)Mutation(s): 0 
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, and viral Rhodopsins
Protein: 
Archaerhodopsin-2 (aR-2)
Find proteins for P29563 (Halobacterium sp. (strain aus-2))
Go to UniProtKB:  P29563
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L4P
Query on L4P

Download SDF File 
Download CCD File 
A
3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL
C46 H95 O8 P
AFYVWQWWQKSZEV-WGOBCRBGSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
RET
Query on RET

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Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
22B
Query on 22B

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A
BACTERIORUBERIN
C50 H76 O4
UVCQMCCIAHQDAF-CUMPQFAQSA-N
 Ligand Interaction
L2P
Query on L2P

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Download CCD File 
A
2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
L3P
Query on L3P

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Download CCD File 
A
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
C46 H94 O11 P2
TZXJQSKPTCRGCA-VZSPAKCESA-L
 Ligand Interaction
SQL
Query on SQL

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Download CCD File 
A
(6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene
squalene
C30 H50
YYGNTYWPHWGJRM-AAJYLUCBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 62.739α = 90.00
b = 62.739β = 90.00
c = 331.464γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
ADSCdata collection
CNSrefinement
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-27 
  • Released Date: 2014-10-15 
  • Deposition Author(s): Kouyama, T.

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release