3M4E

Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 

wwPDB Validation   3D Report Full Report


This is version 2.2 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 U S A 107: 8165-8170

  • DOI: https://doi.org/10.1073/pnas.0914229107
  • Primary Citation of Related Structures:  
    3M2L, 3M3R, 3M4D, 3M4E

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-hemolysin
A, B, C, D, E
A, B, C, D, E, F, G
293Staphylococcus aureusMutation(s): 1 
Gene Names: hlahly
Membrane Entity: Yes 
UniProt
Find proteins for P09616 (Staphylococcus aureus)
Explore P09616 
Go to UniProtKB:  P09616
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09616
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
H
7N/A
Glycosylation Resources
GlyTouCan:  G01435GL
GlyCosmos:  G01435GL
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.35α = 90
b = 134.27β = 90.97
c = 132.06γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-06
    Changes: Advisory, Database references, Structure summary
  • Version 2.2: 2024-02-21
    Changes: Data collection