Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Observed: 0.155 

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Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities.

Buckle, A.M.Cramer, P.Fersht, A.R.

(1996) Biochemistry 35: 4298-4305

  • DOI: https://doi.org/10.1021/bi9524676
  • Primary Citation of Related Structures:  
    1BRH, 1BRI, 1BRJ, 1BRK

  • PubMed Abstract: 

    We have solved the 2.0-A resolution crystal structures of four cavity-creating Ile/Leu-->Ala mutations in the hydrophobic core of barnase and compare and contrast the structural responses to mutation with those found for Leu-->Ala mutations in T4 lysozyme. First, there are rearrangements of structure of barnase that cause the cavities to collapse partly, and there is an approximately linear relationship between the changes in stability and the volume of the cavity similar to that found for the mutants of T4 lysozyme. Second, although it is currently accepted that hydrophobic cavities formed on the mutation of large hydrophobic side chains to smaller ones are not occupied by water molecules, we found a buried water molecule in the crystal structure of the barnase mutant Ile76-->Ala. A single hydrogen bond is formed between the water molecule and a polar atom, the carbonyl oxygen of Phe7, in the hydrophobic cavity that is formed on mutation. A survey of hydrophobic cavities produced by similar mutations in different proteins reveals that they all contain a proportion of polar atoms in their linings. The availability of such polar sites has implications for understanding folding pathways because a solvated core is presumed present in the transition state for folding and unfolding. Notably, the hydrogen bond between the cavity-water and the carbonyl group of Phe7 is also a marked early feature of very recent molecular dynamics simulations of barnase denaturation [Caflisch, A., & Karplus, M. (1995) J. Mol. Biol. 252, 672-708]. It is possible that cavities engineered into the hydrophobic cores of other proteins may contain water molecules, even though they cannot be detected by crystallographic analysis.

  • Organizational Affiliation

    Centre for Protein Engineering, Medical Research Council Centre, Cambridge, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
110Bacillus amyloliquefaciensMutation(s): 0 
EC: 3.1.27
Find proteins for P00648 (Bacillus amyloliquefaciens)
Explore P00648 
Go to UniProtKB:  P00648
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00648
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
D [auth C]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Observed: 0.155 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.8α = 90
b = 58.8β = 90
c = 81.68γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other