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: 2.13 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.cgd.6b00950
  • Primary Citation of Related Structures:  
    5KKH, 5KKI, 5KKJ, 5KKK

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin-I
A, B, C
268Haloquadratum walsbyi DSM 16790Mutation(s): 0 
Gene Names: bop1bopIHQ_1014A
Membrane Entity: Yes 
UniProt
Find proteins for Q18DH8 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001))
Explore Q18DH8 
Go to UniProtKB:  Q18DH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18DH8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A]
F [auth A]
H [auth B]
I [auth B]
L [auth C]
D [auth A],
F [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.11α = 90
b = 61.27β = 116.26
c = 119.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description