1EZG | pdb_00001ezg

CRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO MOLITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.200 (Depositor) 
  • R-Value Work: 
    0.161 (Depositor) 
  • R-Value Observed: 
    0.160 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1EZG

This is version 1.3 of the entry. See complete history

Literature

Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein.

Liou, Y.C.Tocilj, A.Davies, P.L.Jia, Z.

(2000) Nature 406: 322-324

  • DOI: https://doi.org/10.1038/35018604
  • Primary Citation Related Structures: 
    1EZG

  • PubMed Abstract: 

    Insect antifreeze proteins (AFP) are much more effective than fish AFPs at depressing solution freezing points by ice-growth inhibition. AFP from the beetle Tenebrio molitor is a small protein (8.4 kDa) composed of tandem 12-residue repeats (TCTxSxxCxxAx). Here we report its 1.4-A resolution crystal structure, showing that this repetitive sequence translates into an exceptionally regular beta-helix. Not only are the 12-amino-acid loops almost identical in the backbone, but also the conserved side chains are positioned in essentially identical orientations, making this AFP perhaps the most regular protein structure yet observed. The protein has almost no hydrophobic core but is stabilized by numerous disulphide and hydrogen bonds. On the conserved side of the protein, threonine-cysteine-threonine motifs are arrayed to form a flat beta-sheet, the putative ice-binding surface. The threonine side chains have exactly the same rotameric conformation and the spacing between OH groups is a near-perfect match to the ice lattice. Together with tightly bound co-planar external water, three ranks of oxygen atoms form a two-dimensional array, mimicking an ice section.


  • Organizational Affiliation
    • Department of Biochemistry, Queen's University, Kingston, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 16.78 kDa 
  • Atom Count: 1,106 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THERMAL HYSTERESIS PROTEIN ISOFORM YL-1
A, B
84Tenebrio molitorMutation(s): 0 
Gene Names: CDNA FROM FAT BODY LIBRARY
UniProt
Find proteins for O16119 (Tenebrio molitor)
Explore O16119 
Go to UniProtKB:  O16119
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO16119
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.200 (Depositor) 
  • R-Value Work:  0.161 (Depositor) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.832α = 90
b = 73.832β = 90
c = 53.13γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Structure summary