1UCS

Type III Antifreeze Protein RD1 from an Antarctic Eel Pout


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.62 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.137 

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This is version 1.3 of the entry. See complete history


Literature

The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.

Ko, T.P.Robinson, H.Gao, Y.G.Cheng, C.H.DeVries, A.L.Wang, A.H.

(2003) Biophys J 84: 1228-1237

  • DOI: 10.1016/S0006-3495(03)74938-8
  • Primary Citation of Related Structures:  
    1UCS

  • PubMed Abstract: 
  • RD1 is a 7-kDa globular protein from the Antarctic eel pout Lycodichthys dearborni. It belongs to type III of the four types of antifreeze proteins (AFPs) found in marine fishes living at subzero temperatures. For type III AFP, a potential ice-binding flat surface has been identified and is imbedded with side chains capable of making hydrogen bonds with a specific lattice plane on ice ...

    RD1 is a 7-kDa globular protein from the Antarctic eel pout Lycodichthys dearborni. It belongs to type III of the four types of antifreeze proteins (AFPs) found in marine fishes living at subzero temperatures. For type III AFP, a potential ice-binding flat surface has been identified and is imbedded with side chains capable of making hydrogen bonds with a specific lattice plane on ice. So far, all crystallographic studies on type III AFPs were carried out using the Atlantic ocean pout Macrozoarces americanus as the source organism. Here we present the crystal structure of a type III AFP from a different zoarcid fish, and at an ultra-high resolution of 0.62 A. The protein fold of RD1 comprises a compact globular domain with two internal tandem motifs arranged about a pseudo-dyad symmetry. Each motif of the "pretzel fold" includes four short beta-strands and a 3(10) helix. There is a novel internal cavity of 45 A(3) surrounded by eight conserved nonpolar residues. The model contains several residues with alternate conformations, and a number of split water molecules, probably caused by alternate interactions with the protein molecule. After extensive refinement that includes hydrogen atoms, significant residual electron densities associated with the electrons of peptides and many other bonds could be visualized.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Antifreeze peptide RD1A64Lycodichthys dearborniMutation(s): 0 
UniProt
Find proteins for P35751 (Lycodichthys dearborni)
Explore P35751 
Go to UniProtKB:  P35751
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35751
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.62 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.501α = 90
b = 39.502β = 90
c = 44.64γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-06
    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: 2019-11-06
    Changes: Data collection, Database references