3M3R

Crystal structure of the M113F alpha-hemolysin mutant complexed with beta-cyclodextrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores.

Banerjee, A.Mikhailova, E.Cheley, S.Gu, L.Q.Montoya, M.Nagaoka, Y.Gouaux, E.Bayley, H.

(2010) Proc.Natl.Acad.Sci.USA 107: 8165-8170

  • DOI: 10.1073/pnas.0914229107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro- ...

    Engineered protein pores have several potential applications in biotechnology: as sensor elements in stochastic detection and ultrarapid DNA sequencing, as nanoreactors to observe single-molecule chemistry, and in the construction of nano- and micro-devices. One important class of pores contains molecular adapters, which provide internal binding sites for small molecules. Mutants of the alpha-hemolysin (alphaHL) pore that bind the adapter beta-cyclodextrin (betaCD) approximately 10(4) times more tightly than the wild type have been obtained. We now use single-channel electrical recording, protein engineering including unnatural amino acid mutagenesis, and high-resolution x-ray crystallography to provide definitive structural information on these engineered protein nanopores in unparalleled detail.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-hemolysin
A, B, C, D, E, F, G
293Staphylococcus aureusMutation(s): 1 
Gene Names: hly (hla)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
α-hemolysin
Find proteins for P09616 (Staphylococcus aureus)
Go to UniProtKB:  P09616
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCD
Query on BCD

Download SDF File 
Download CCD File 
F, G
BETA-CYCLODEXTRIN
CYCLO-HEPTA-AMYLOSE
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCDKd: 3000 nM BINDINGMOAD
BCDKd: 480 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 151.670α = 90.00
b = 135.400β = 90.77
c = 133.010γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance