3BOG

Snow Flea Antifreeze Protein Quasi-racemate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 

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:  

  • 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 pr ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6.5 kDa glycine-rich antifreeze protein
A, B
81Hypogastrura harveyiMutation(s): 1 
Find proteins for Q38PT6 (Hypogastrura harveyi)
Go to UniProtKB:  Q38PT6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
6.5 kDa glycine-rich antifreeze protein
C, D
81Hypogastrura harveyiMutation(s): 0 
Find proteins for Q38PT6 (Hypogastrura harveyi)
Go to UniProtKB:  Q38PT6
Small Molecules
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
DCY
Query on DCY
C, D
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DPR
Query on DPR
C, D
D-PEPTIDE LINKINGC5 H9 N O2

--

DLY
Query on DLY
C, D
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DHI
Query on DHI
C, D
D-PEPTIDE LINKINGC6 H10 N3 O2

--

DSN
Query on DSN
C, D
D-PEPTIDE LINKINGC3 H7 N O3

--

DVA
Query on DVA
C, D
D-PEPTIDE LINKINGC5 H11 N O2

--

DTH
Query on DTH
C, D
D-PEPTIDE LINKINGC4 H9 N O3

--

DAL
Query on DAL
C, D
D-PEPTIDE LINKINGC3 H7 N O2

--

DAS
Query on DAS
C, D
D-PEPTIDE LINKINGC4 H7 N O4

--

DSG
Query on DSG
C, D
D-PEPTIDE LINKINGC4 H8 N2 O3

--

SYS
Query on SYS
A, B
L-PEPTIDE LINKINGC5 H10 N2 O3 SeCYS
DAR
Query on DAR
C, D
D-PEPTIDE LINKINGC6 H15 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 28.640α = 88.62
b = 32.359β = 89.31
c = 59.699γ = 72.84
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling
RESOLVEphasing
REFMACrefinement
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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