4KE2 | pdb_00004ke2

Crystal structure of the hyperactive Type I antifreeze from winter flounder

• PDB DOI: https://doi.org/10.2210/pdb4KE2/pdb

• Classification: ANTIFREEZE PROTEIN
• Organism(s): Pseudopleuronectes americanus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-25 Released: 2014-02-26 
• Deposition Author(s): Sun, T., Lin, F.-H., Campbell, R.L., Allingham, J.S., Davies, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.

Sun, T., Lin, F.H., Campbell, R.L., Allingham, J.S., Davies, P.L.

(2014) Science 343: 795-798

• PubMed: 24531972 
• DOI: https://doi.org/10.1126/science.1247407
• Primary Citation Related Structures: 
  4KE2


• PubMed Abstract: 
  

  When polypeptide chains fold into a protein, hydrophobic groups are compacted in the center with exclusion of water. We report the crystal structure of an alanine-rich antifreeze protein that retains ~400 waters in its core. The putative ice-binding residues of this dimeric, four-helix bundle protein point inwards and coordinate the interior waters into two intersecting polypentagonal networks. The bundle makes minimal protein contacts between helices, but is stabilized by anchoring to the semi-clathrate water monolayers through backbone carbonyl groups in the protein interior. The ordered waters extend outwards to the protein surface and likely are involved in ice binding. This protein fold supports both the anchored-clathrate water mechanism of antifreeze protein adsorption to ice and the water-expulsion mechanism of protein folding.

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Organizational Affiliation: 
• Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.48 kDa 
• Atom Count: 5,412 
• Modeled Residue Count: 588 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I hyperactive antifreeze protein	A, B, C	196	Pseudopleuronectes americanus	Mutation(s): 0
UniProt
Find proteins for B1P0S1 (Pseudopleuronectes americanus) Explore B1P0S1  Go to UniProtKB:  B1P0S1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.82	α = 90
b = 48.14	β = 91.87
c = 182.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SHARP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Sun, T., Lin, F.-H., Campbell, R.L., Allingham, J.S., Davies, P.L.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references