1AEX

STAPHYLOCOCCAL NUCLEASE, METHANE THIOL DISULFIDE TO V23C VARIANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.

Wynn, R.Harkins, P.C.Richards, F.M.Fox, R.O.

(1996) Protein Sci 5: 1026-1031

  • DOI: 10.1002/pro.5560050605
  • Primary Citation of Related Structures:  
    2NUC, 3NUC, 5NUC, 1A2U, 1A2T, 1AEX, 1NUC

  • PubMed Abstract: 
  • The structures of several variants of staphylococcal nuclease with long flexible unnatural amino acid side chains in the hydrophobic core have been determined by X-ray crystallography. The unnatural amino acids are disulfide moieties between the lone cysteine residue in V23C nuclease and methane, ethane, 1-n-propane, 1-n-butane, 1-n-pentane, and 2-hydroxyethyl thiols ...

    The structures of several variants of staphylococcal nuclease with long flexible unnatural amino acid side chains in the hydrophobic core have been determined by X-ray crystallography. The unnatural amino acids are disulfide moieties between the lone cysteine residue in V23C nuclease and methane, ethane, 1-n-propane, 1-n-butane, 1-n-pentane, and 2-hydroxyethyl thiols. We have examined changes in the core packing of these mutants. Side chains as large as the 1-n-propyl cysteine disulfide can be incorporated without perturbation of the structure. This is due, in part, to cavities present in the wild-type protein. The longest side chains are not well defined, even though they remain buried within the protein interior. These results suggest that the enthalpy-entropy balance that governs the rigidity of protein interiors favors tight packing only weakly. Additionally, the tight packing observed normally in protein interiors may reflect, in part, the limited numbers of rotamers available to the natural amino acids.


    Related Citations: 
    • Interactions in Nonnative and Truncated Forms of Staphylococcal Nuclease as Indicated by Mutational Free Energy Changes
      Wynn, R., Anderson, C.L., Richards, F.M., Fox, R.O.
      (1995) Protein Sci 4: 1815
    • Unnatural Amino Acid Packing Mutants of Escherichia Coli Thioredoxin Produced by Combined Mutagenesis/Chemical Modification Techniques
      Wynn, R., Richards, F.M.
      (1993) Protein Sci 2: 395

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA. wynnr@al.lldmpc.umc.dupont.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
STAPHYLOCOCCAL NUCLEASEA149Staphylococcus aureusMutation(s): 1 
Gene Names: nuc
EC: 3.1.31.1
UniProt
Find proteins for P00644 (Staphylococcus aureus)
Explore P00644 
Go to UniProtKB:  P00644
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THP (Subject of Investigation/LOI)
Query on THP

Download Ideal Coordinates CCD File 
C [auth A]THYMIDINE-3',5'-DIPHOSPHATE
C10 H16 N2 O11 P2
CSNCBOPUCJOHLS-XLPZGREQSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
AL-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.6α = 90
b = 48.6β = 90
c = 63.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-06-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance