› 5b35

X-ray diffraction
2.35Å resolution

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Released:
DOI: 10.2210/pdb5b35/pdb
PDB entry 5b35 coloured by chain, front view.
PDB entry 5b35 coloured by chain, side view.
PDB entry 5b35 coloured by chain, top view.
Source organism: Halobacterium salinarum
Primary publication:
Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.
Nakane T, Hanashima S, Suzuki M, Saiki H, Hayashi T, Kakinouchi K, Sugiyama S, Kawatake S, Matsuoka S, Matsumori N, Nango E, Kobayashi J, Shimamura T, Kimura K, Mori C, Kunishima N, Sugahara M, Takakyu Y, Inoue S, Masuda T, Hosaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Inoue T, Nureki O, Iwata S, Murata M, Mizohata E
Proc Natl Acad Sci U S A 113 13039-13044 (2016)
PMID: 27799539

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-109192 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bacteriorhodopsin Chain: A
Molecule details ›
Chain: A
Length: 249 amino acids
Theoretical weight: 26.93 KDa
Source organism: Halobacterium salinarum
UniProt:
  • Canonical: B0R5N9 (Residues: 14-262; Coverage: 95%)
Gene names: OE_3106F, bop
Sequence domains: Bacteriorhodopsin-like protein
Structure domains: Rhodopsin 7-helix transmembrane proteins

Ligands and Environments

8 bound ligands:
Ligand RET 1 x RET
Ligand 4QM 1 x 4QM
Ligand OCT 1 x OCT
Ligand D10 5 x D10
Ligand D12 3 x D12
Ligand R16 2 x R16
Ligand HP6 2 x HP6
Ligand DD9 2 x DD9
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SACLA BEAMLINE BL3
Spacegroup: C2221
Unit cell:
a: 46.2Å b: 103Å c: 128.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.166 0.22

Quick links

Citations

7 review citations

A Bright Future for Serial Femtosecond Crystallography with XFELs.
Johansson et al. (2017)
6 more

2 mentions without citation

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.
Enkavi et al. (2019)
1 more