103L

HOW AMINO-ACID INSERTIONS ARE ALLOWED IN AN ALPHA-HELIX OF T4 LYSOZYME

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme.

Heinz, D.W., Baase, W.A., Dahlquist, F.W., Matthews, B.W.

(1993) Nature 361: 561-564

  • DOI: 10.1038/361561a0
  • Primary Citation of Related Structures:  
    102L, 103L, 104L, 201L, 205L

  • PubMed Abstract: 

    • Studies of extant protein sequences indicate that amino-acid insertions and deletions are preferentially located in loop regions, which has traditionally been explained as the result of selection removing deleterious mutations within secondary structural elements from the population ...

    Studies of extant protein sequences indicate that amino-acid insertions and deletions are preferentially located in loop regions, which has traditionally been explained as the result of selection removing deleterious mutations within secondary structural elements from the population. But there is no a priori reason to discount the possibility that insertions within secondary structure could either be tolerated until compensatory mutations arise, or have effects that are propagated away from secondary structure into loops. Earlier studies have indicated that insertions are generally tolerated, although much less well within secondary structure elements than in loop regions. Here we show that amino-acid insertions in an alpha-helix of T4 lysozyme can be accepted in two different ways. In some cases the inserted amino acids are accommodated within the helix, leading to the translocation of wild-type residues from the helix to the preceding loop. In other cases the insertion causes a 'looping-out' in the first or last turn of the helix. The individual structural responses seem to be dominated by the maintenance of the interface between the helix and the rest of the protein.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T4 LYSOZYMEA167Escherichia virus T4Mutation(s): 0 
Gene Names: E
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BME
Query on BME
Download Ideal Coordinates CCD File 
D [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.9α = 90
b = 60.9β = 90
c = 95.6γ = 120
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance