5B34

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with Iodine-labeled Detergent HAD13a Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 5B34

Classification: PROTON TRANSPORT

Total Structure Weight: 30704.20

Macromolecule Entities
Molecule Chains Length Organism Details
Bacteriorhodopsin A 249 Halobacterium salinarum Gene Name(s): bop VNG_1467G
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Bacterial and Algal Rhodopsins

Protein Name: Bacteriorhodopsin (BR)


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4QL
Query on 4QL

A 2,4,6-tris(iodanyl)-5-(octanoylamino)benzene- 1,3-dicarboxylic acid
C16 H18 I3 N O5
STMIUHPXRYKWPU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RET
Query on RET

A RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
R16
Query on R16

A HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D12
Query on D12

A DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D10
Query on D10

A DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DD9
Query on DD9

A nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OCT
Query on OCT

A N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HP6
Query on HP6

A HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.163
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 46.20 α = 90.00
b = 103.00 β = 90.00
c = 128.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-02-10
  • Released Date: 2016-11-09
  • Deposition author(s): Mizohata, E., Nakane, T.

Revision History

  • 2016-11-16
    Type: Database references
  • 2016-11-30
    Type: Database references