1HG7

High resolution structure of HPLC-12 type III antifreeze protein from Ocean Pout Macrozoarces americanus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Understanding the Mechanism of Ice Binding by Type III Antifreeze Protein

Antson, A.A.Smith, D.J.Roper, D.I.Lewis, S.Caves, L.S.D.Verma, C.S.Buckley, S.L.Lillford, P.J.Hubbard, R.E.

(2001) J.Mol.Biol. 305: 875

  • DOI: 10.1006/jmbi.2000.4336
  • Also Cited By: 5C7R

  • PubMed Abstract: 
  • Type III antifreeze proteins (AFPs) are present in the body fluids of some polar fishes where they inhibit ice growth at subzero temperatures. Previous studies of the structure of type III AFP by NMR and X-ray identified a remarkably flat surface on ...

    Type III antifreeze proteins (AFPs) are present in the body fluids of some polar fishes where they inhibit ice growth at subzero temperatures. Previous studies of the structure of type III AFP by NMR and X-ray identified a remarkably flat surface on the protein containing amino acids that were demonstrated to be important for interaction with ice by mutational studies. It was proposed that this protein surface binds onto the (1 0 [\bar 1] 0) plane of ice with the key amino acids interacting directly with the water molecules in the ice crystal. Here, we show that the mechanism of type III AFP interaction with ice crystals is more complex than that proposed previously. We report a high-resolution X-ray structure of type III AFP refined at 1.15 A resolution with individual anisotropic temperature factors. We report the results of ice-etching experiments that show a broad surface coverage, suggesting that type III AFP binds to a set of planes that are parallel with or inclined at a small angle to the crystallographic c-axis of the ice crystal. Our modelling studies, performed with the refined structure, confirm that type III AFP can make energetically favourable interactions with several ice surfaces.


    Organizational Affiliation

    Structural Biology Laboratory Department of Chemistry, University of York, Heslington, York Y01 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HPLC-12 TYPE III ANTIFREEZE PROTEIN
A
66Zoarces americanusMutation(s): 2 
Find proteins for P19614 (Zoarces americanus)
Go to UniProtKB:  P19614
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.218α = 90.00
b = 39.127β = 90.00
c = 44.694γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
CCP4data scaling
SHELXLphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-31
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Data collection, Database references, Derived calculations, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-07-24
    Type: Data collection