Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme.

Baldwin, E.Xu, J.Hajiseyedjavadi, O.Baase, W.A.Matthews, B.W.

(1996) J Mol Biol 259: 542-559

  • DOI: 10.1006/jmbi.1996.0338
  • Primary Citation of Related Structures:  
    195L, 196L, 197L, 198L, 199L, 200L

  • PubMed Abstract: 
  • Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating ...

    Previous analysis of randomly generated multiple mutations within the core of bacteriophage T4 lysozyme suggested that the "large-to-small" substitution Leu121 to Ala (L121A) and the spatially adjacent "small-to-large" substitution Ala129 to Met (A129M) might be mutually compensating. To test this hypothesis, the individual variants L121A and A129M were generated, as well as the double "size-switch" mutant L121A/A129M. To make the interchange symmetrical, the combination of L121A with A129L to give L121A/A129L was also constructed. The single mutations were all destabilizing. Somewhat surprisingly, the small-to-large substitutions, which increase hydrophobic stabilization but can also introduce strain, were less deleterious than the large-to-small replacements. Both Ala129 --> Leu and Ala129 --> Met offset the destabilization of L121A by about 50%. Also, in contrast to typical Leu --> Ala core substitutions, which destabilize by 2 to 5 kcal/mol, Leu121 --> Ala slightly stabilized A129L and A129M. Crystal structure analysis showed that a combination of side-chain and backbone adjustments partially accommodated changes in side-chain volume, but only to a limited degree. For example, the cavity that was created by the Leu121 to Ala replacement actually became larger in L121A/A129L. The results demonstrate that the destabilization associated with a change in volume of one core residue can be specifically compensated by an offsetting volume change in an adjacent residue. It appears, however, that complete compensation is unlikely because it is difficult to reconstitute an equivalent set of interactions. The relatively slow evolution of core relative to surface residues appears, therefore, to be due to two factors. First, a mutation in a single core residue that results in a substantial change in size will normally lead to a significant loss in stability. Such mutations will presumably be selected against. Second, if a change in bulk does occur in a buried residue, it cannot normally be fully compensated by a mutation of an adjacent residue. Thus, the most probable response will tend to be reversion to the parent protein.

    Related Citations: 
    • The Role of Backbone Flexibility in the Accommodation of Variants that Repack the Core of T4 Lysozyme
      Baldwin, E.P., Hajiseyedjavadi, O., Baase, W.A., Matthews, B.W.
      (1993) Science 262: 1715
    • Control of Enzyme Activity by an Engineered Disulfide Bond
      Matsumura, M., Matthews, B.W.
      (1989) Science 243: 792
    • Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance
      Muchmore, D.C., Mcintosh, L.P., Russell, C.B., Anderson, D.E., Dahlquist, F.W.
      (1989) Methods Enzymol 177: 44
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
      Weaver, L.H., Matthews, B.W.
      (1987) J Mol Biol 193: 189

    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene, 97403, USA.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYMEA164Escherichia virus T4Mutation(s): 0 
Gene Names: E
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on BME

Download Ideal Coordinates CCD File 
C2 H6 O S
 Ligand Interaction
Query on CL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CHLORIDE ION
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Observed: 0.158 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.1α = 90
b = 61.1β = 90
c = 96.1γ = 120
Software Package:
Software NamePurpose
XUONG-HAMLINdata reduction
Xengen (HOWARD, NIELSEN, XUONG)data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2020-07-22
    Changes: Data collection, Database references, Other, Refinement description