1LLI

THE CRYSTAL STRUCTURE OF A MUTANT PROTEIN WITH ALTERED BUT IMPROVED HYDROPHOBIC CORE PACKING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of a mutant protein with altered but improved hydrophobic core packing.

Lim, W.A.Hodel, A.Sauer, R.T.Richards, F.M.

(1994) Proc.Natl.Acad.Sci.USA 91: 423-427


  • PubMed Abstract: 
  • The dense packing observed in protein interiors appears to be crucial for stabilizing the native structure--even subtle internal substitutions are usually destabilizing. Thus, steric complementarity of core residues is thought to be an important crit ...

    The dense packing observed in protein interiors appears to be crucial for stabilizing the native structure--even subtle internal substitutions are usually destabilizing. Thus, steric complementarity of core residues is thought to be an important criterion for "inverse folding" predictive methods, which judge whether a newly determined sequence is consistent with any known folds. A major problem in the development of useful core packing evaluation algorithms, however, is that there are occasional mutations that are predicted to disrupt native packing but that yield an equally or more stable protein. We have solved the crystal structure of such a variant of lambda repressor, which, despite having three larger core substitutions, is more stable than the wild type. The structure reveals that the protein accommodates the potentially disruptive residues with shifts in its alpha-helical arrangement. The variant is apparently more stable because its packing is improved--the core has a higher packing density and little geometric strain. These rearrangements, however, cause repositioning of functional residues, which result in reduced DNA binding activity. By comparing these results with the predictions of two core packing algorithms, it is clear that the protein possesses a relatively high degree of main-chain flexibility that must be accounted for in order to predict the full spectrum of compatible core sequences. This study also shows how, in protein evolution, a particular set of core residue identities might be selected not because they provide optimal stability but because they provide sufficient stability in addition to the precise structure required for optimal activity.


    Related Citations: 
    • Refined 1.8 Angstrom Crystal Structure of the Lambda Repressor-Operator Complex
      Beamer, L.J.,Pabo, C.O.
      (1992) J.Mol.Biol. 227: 177


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LAMBDA REPRESSOR)
A, B
92Enterobacteria phage lambdaGene Names: cI
Find proteins for P03034 (Enterobacteria phage lambda)
Go to UniProtKB:  P03034
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*AP*CP*CP*AP*CP*TP*GP*GP*CP*GP*GP*TP*GP*A P*TP*AP*T)-3')D20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*TP*CP*AP*CP*CP*GP*CP*CP*AP*GP*TP*GP*G P*TP*AP*T)-3')E20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.150α = 90.00
b = 68.900β = 92.20
c = 56.790γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations