› 1dze

X-ray diffraction
2.5Å resolution

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Released:
DOI: 10.2210/pdb1dze/pdb
PDB entry 1dze coloured by chain, front view.
PDB entry 1dze coloured by chain, side view.
PDB entry 1dze coloured by chain, top view.
Source organism: Halobacterium salinarum
Primary publication:
Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix.
Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T
J Mol Biol 341 1023-37 (2004)
PMID: 15328615

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136413 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Bacteriorhodopsin Chain: A
Molecule details ›
Chain: A
Length: 248 amino acids
Theoretical weight: 26.81 KDa
Source organism: Halobacterium salinarum
UniProt:
  • Canonical: P02945 (Residues: 14-261; Coverage: 95%)
Gene names: VNG_1467G, bop
Sequence domains: Bacteriorhodopsin-like protein
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, MAN, GAL
Carbohydrate polymer
5 bound ligands:
Ligand RET 1 x RET
Ligand L1P 1 x L1P
Ligand L2P 2 x L2P
Ligand L3P 1 x L3P
Ligand L4P 1 x L4P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P622
Unit cell:
a: 102.4Å b: 102.4Å c: 112.3Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.257 0.257 0.283

Quick links

Citations

6 review citations

The role of protein-bound water molecules in microbial rhodopsins.
Gerwert et al. (2014)
5 more

3 mentions without citation

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.
Nogly et al. (2016)
2 more