1JQU

Are Carboxy Terminii of Helices Coded by the Local Sequence or by Tertiary Structure Contacts


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A test of proposed rules for helix capping: Implications for protein design

Sagermann, M.Martensson, L.-G.Baase, W.A.Matthews, B.W.

(2002) Protein Sci. 11: 516-521

  • DOI: 10.1110/ps.39802
  • Primary Citation of Related Structures:  1JOZ, 1LLH

  • PubMed Abstract: 
  • alpha-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative alpha(L) motif. Rose and coworkers developed stereochemical rules ...

    alpha-helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative alpha(L) motif. Rose and coworkers developed stereochemical rules to identify the locations of such motifs in proteins of unknown structure based only on their amino acid sequences. To check the effectiveness of these rules, they made specific predictions regarding the structural and thermodynamic consequences of certain mutations in T4 lysozyme. We have constructed these mutants and show here that they have neither the structure nor the stability that was predicted. The results show the complexity of the protein-folding problem. Comparison of known protein structures may show that a characteristic sequence of amino acids (a sequence motif) corresponds to a conserved structural motif. In any particular protein, however, changes in other parts of the sequence may result in a different conformation. The structure is determined by sequence as a whole, not by parts considered in isolation.


    Related Citations: 
    • Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution.
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189
    • The alpha-L Conformations at the Ends of Helices
      Schellman, C.
      (1980) Protein Folding --: 53
    • Rules for alpha-helix termination by glycine.
      Aurora, R.,Srinivasan, R.,Rose, G.D.
      (1994) Science 264: 1126


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B, C, D
164Enterobacteria phage T4Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.300α = 90.00
b = 77.200β = 90.00
c = 138.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
TNTphasing
CNSphasing
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-03-26
    Type: Database references
  • Version 1.4: 2017-10-04
    Type: Refinement description