› 6kfq

X-ray diffraction
1.84Å resolution

Crystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus

Released:
DOI: 10.2210/pdb6kfq/pdb
PDB entry 6kfq coloured by chain, front view.
PDB entry 6kfq coloured by chain, side view.
PDB entry 6kfq coloured by chain, top view.
Source organism: Rubrobacter xylanophilus DSM 9941
Primary publication:
How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?
Hayashi T, Yasuda S, Suzuki K, Akiyama T, Kanehara K, Kojima K, Tanabe M, Kato R, Senda T, Sudo Y, Murata T, Kinoshita M
J Phys Chem B 124 990-1000 (2020)
PMID: 31955569

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172777 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Rhodopsin Chain: A
Molecule details ›
Chain: A
Length: 239 amino acids
Theoretical weight: 25.85 KDa
Source organism: Rubrobacter xylanophilus DSM 9941
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1AUE6 (Residues: 1-239; Coverage: 100%)
Gene name: Rxyl_2037
Sequence domains: Bacteriorhodopsin-like protein

Ligands and Environments

3 bound ligands:
Ligand MPG 16 x MPG
Ligand RET 1 x RET
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P212121
Unit cell:
a: 29.93Å b: 68.41Å c: 107.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.226
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.
de Grip et al. (2022)
5 other articles

3 mentions without citation

Applicability of Styrene-Maleic Acid Copolymer for Two Microbial Rhodopsins, RxR and HsSRI.
Ueta et al. (2020)
2 more