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
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(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