3BOG

Snow Flea Antifreeze Protein Quasi-racemate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers

Pentelute, B.L.Gates, Z.P.Tereshko, V.Dashnau, J.L.Vanderkooi, J.M.Kossiakoff, A.A.Kent, S.B.

(2008) J Am Chem Soc 130: 9695-9701

  • DOI: 10.1021/ja8013538
  • Primary Citation of Related Structures:  
    2PNE, 3BOI, 3BOG

  • PubMed Abstract: 
  • Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the chemically synthesized protei ...

    Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the chemically synthesized proteins d-sfAFP and l-sfAFP occurred much more readily than for l-sfAFP alone. More facile crystal formation also occurred from a quasi-racemic mixture of d-sfAFP and l-Se-sfAFP, a chemical protein analogue that contains an additional -SeCH2- moiety at one residue and thus differs slightly from the true enantiomer. Multiple wavelength anomalous dispersion (MAD) phasing from quasi-racemate crystals was then used to determine the X-ray structure of the sfAFP protein molecule. The resulting model was used to solve by molecular replacement the X-ray structure of l-sfAFP to a resolution of 0.98 A. The l-sfAFP molecule is made up of six antiparallel left-handed PPII helixes, stacked in two sets of three, to form a compact brick-like structure with one hydrophilic face and one hydrophobic face. This is a novel experimental protein structure and closely resembles a structural model proposed for sfAFP. These results illustrate the utility of total chemical synthesis combined with racemic crystallization and X-ray crystallography for determining the unknown structure of a protein.


    Organizational Affiliation

    Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6.5 kDa glycine-rich antifreeze protein AB81Hypogastrura harveyiMutation(s): 1 
Find proteins for Q38PT6 (Hypogastrura harveyi)
Explore Q38PT6 
Go to UniProtKB:  Q38PT6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
6.5 kDa glycine-rich antifreeze protein CD81Hypogastrura harveyiMutation(s): 0 
Find proteins for Q38PT6 (Hypogastrura harveyi)
Explore Q38PT6 
Go to UniProtKB:  Q38PT6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNL
Query on UNL

Download Ideal Coordinates CCD File 
B
Unknown ligand
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SYS
Query on SYS
A,BL-PEPTIDE LINKINGC5 H10 N2 O3 SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.64α = 88.62
b = 32.359β = 89.31
c = 59.699γ = 72.84
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-01-24
    Changes: Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-08-21
    Changes: Advisory, Data collection, Derived calculations