1KFM

Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Core side-chain packing and backbone conformation in Lpp-56 coiled-coil mutants.

Liu, J.Cao, W.Lu, M.

(2002) J Mol Biol 318: 877-888

  • DOI: 10.1016/S0022-2836(02)00138-9
  • Primary Citation of Related Structures:  
    1KFM, 1KFN

  • PubMed Abstract: 
  • Native proteins exhibit precise geometric packing of atoms in their hydrophobic interiors. Nonetheless, controversy remains about the role of core side-chain packing in specifying and stabilizing the folded structures of proteins. Here we investigate the role of core packing in determining the conformation and stability of the Lpp-56 trimerization domain ...

    Native proteins exhibit precise geometric packing of atoms in their hydrophobic interiors. Nonetheless, controversy remains about the role of core side-chain packing in specifying and stabilizing the folded structures of proteins. Here we investigate the role of core packing in determining the conformation and stability of the Lpp-56 trimerization domain. The X-ray crystal structures of Lpp-56 mutants with alanine substitutions at two and four interior core positions reveal trimeric coiled coils in which the twist of individual helices and the helix-helix spacing vary significantly to achieve the most favored superhelical packing arrangement. Introduction of each alanine "layer" into the hydrophobic core destabilizes the superhelix by 1.4 kcal mol(-1). Although the methyl groups of the alanine residues pack at their optimum van der Waals contacts in the coiled-coil trimer, they provide a smaller component of hydrophobic interactions than bulky hydrophobic side-chains to the thermodynamic stability. Thus, specific side-chain packing in the hydrophobic core of coiled coils are important determinants of protein main-chain conformation and stability.


    Organizational Affiliation

    Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR OUTER MEMBRANE LIPOPROTEINA56Escherichia coliMutation(s): 2 
UniProt
Find proteins for P69776 (Escherichia coli (strain K12))
Explore P69776 
Go to UniProtKB:  P69776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69776
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.057α = 90
b = 37.057β = 90
c = 81.912γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MADNESSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2001-11-21 
  • Released Date: 2002-06-28 
  • Deposition Author(s): Liu, J., Cao, W., Lu, M.

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Refinement description