3K55

Structure of beta hairpin deletion mutant of beta toxin from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a mutant beta toxin from Staphylococcus aureus reveals domain swapping and conformational flexibility

Kruse, A.C.Huseby, M.J.Shi, K.Digre, J.Ohlendorf, D.H.Earhart, C.A.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 438-441

  • DOI: 10.1107/S1744309111005239
  • Primary Citation of Related Structures:  
    3K55

  • PubMed Abstract: 
  • The 3.35 Å resolution crystal structure of a mutant form of the staphylococcal sphingomyelinase β toxin in which a conserved hydrophobic β-hairpin has been deleted is reported. It is shown that this mutation induces domain swapping of a C-terminal β-strand, leading to the formation of dimers linked by a conformationally flexible hinge region ...

    The 3.35 Å resolution crystal structure of a mutant form of the staphylococcal sphingomyelinase β toxin in which a conserved hydrophobic β-hairpin has been deleted is reported. It is shown that this mutation induces domain swapping of a C-terminal β-strand, leading to the formation of dimers linked by a conformationally flexible hinge region. Eight dimers are seen in the asymmetric unit, exhibiting a broad spectrum of conformations trapped in place by intermolecular contacts within the crystal lattice. Furthermore, the 16 monomers within each asymmetric unit exhibit a remarkable heterogeneity in thermal factors, which can be accounted for by the varying degrees to which each monomer interacts with other molecules in the crystal. This structure provides a unique example of the challenges associated with crystallographic study of flexible proteins.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-hemolysin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
306Staphylococcus aureus subsp. aureus RN4220Mutation(s): 0 
Gene Names: hlb
EC: 3.1.4.12
UniProt
Find proteins for A7LAI8 (Staphylococcus aureus)
Explore A7LAI8 
Go to UniProtKB:  A7LAI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7LAI8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth B],
S [auth D],
T [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
R [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.377α = 90
b = 134.473β = 116.89
c = 156.99γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance