1KFM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR OUTER MEMBRANE LIPOPROTEIN
A
56Escherichia coli (strain K12)Gene Names: lpp (mlpA, mulI)
Find proteins for P69776 (Escherichia coli (strain K12))
Go to UniProtKB:  P69776
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.260 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 37.057α = 90.00
b = 37.057β = 90.00
c = 81.912γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
MADNESdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2002-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance