Structure of S. nuclease quintuple mutant V23I/V66L/I72L/I92L/V99L

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 

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Proteins with simplified hydrophobic cores compared to other packing mutants.

Chen, J.Lu, Z.Sakon, J.Stites, W.E.

(2004) Biophys Chem 110: 239-248

  • DOI: https://doi.org/10.1016/j.bpc.2004.02.007
  • Primary Citation of Related Structures:  
    1IHZ, 1II3

  • PubMed Abstract: 

    Efforts to design proteins with greatly reduced sequence diversity have often resulted in proteins with so-called molten globule properties. Substitutions were made at six neighboring sites in the major hydrophobic core of staphylococcal nuclease to create variants with all leucine, all isoleucine or all valine at these sites. The mutant proteins with simplified cores constructed here are quite unstable and have poorly packed cores, attested to by interaction energies. Eight related mutants with greater sequence diversity were also constructed. Comparison to these mutants and 159 other permutations of these 3 aliphatic side chains at these same 6 sites previously constructed shows that the simplified cores are not unusual in their stabilities or interaction energies. Further, crystal structures of the two mutants with the worst packing, as measured by interaction energies, showed no unusual disorder in the core. Therefore, reduction of sequence diversity is not necessarily incompatible with a single stable native structure. Other factors must also contribute to previous protein design failures.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arkansas, CHEM 101, Fayetteville, AR 72701-1201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STAPHYLOCOCCAL NUCLEASE149Staphylococcus aureusMutation(s): 5 
Find proteins for P00644 (Staphylococcus aureus)
Explore P00644 
Go to UniProtKB:  P00644
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00644
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.200 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.951α = 90
b = 47.951β = 90
c = 63.77γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection
  • Version 1.5: 2024-04-03
    Changes: Refinement description