5KKH

2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.125 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals.

Broecker, J.Klingel, V.Ou, W.L.Balo, A.R.Kissick, D.J.Ogata, C.M.Kuo, A.Ernst, O.P.

(2016) Cryst Growth Des 16: 6318-6326

  • DOI: 10.1021/acs.cgd.6b00950
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantl ...

    In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi . In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.


    Organizational Affiliation

    Department of Biochemistry and Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada.,GM/CA at Advanced Photon Source, Argonne National Laboratory , Lemont, Illinois 60439, United States.,Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Biochemistry and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin-I
A, B, C
268Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)Mutation(s): 0 
Gene Names: bop1 (bopI)
Find proteins for Q18DH8 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001))
Go to UniProtKB:  Q18DH8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

Download SDF File 
Download CCD File 
A, B, C
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, B, C
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.125 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.110α = 90.00
b = 61.270β = 116.26
c = 119.030γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Government of CanadaCanadaCanada Excellence Research Chair
German Research Foundation (DFG)GermanyBR 5124/1-1

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references