3BOG

Snow Flea Antifreeze Protein Quasi-racemate

Summary for 3BOG

• Entry DOI: 10.2210/pdb3bog/pdb
• Related: 2PNE 3BOI
• Descriptor: 6.5 kDa glycine-rich antifreeze protein, UNKNOWN LIGAND, ... (4 entities in total)
• Functional Keywords: quasi-racemate, sfafp, mirror image proteins, racemic protein crystallography, antifreeze protein
• Biological source: Hypogastrura harveyi; More
• Total number of polymer chains: 4
• Total formula weight: 26139.18

Authors

Pentelute, B.L.,Kent, S.B.H.,Gates, Z.P.,Tereshko, V.,Kossiakoff, A.A.,Kurutz, J.,Dashnau, J.,Vaderkooi, J.M. (deposition date: 2007-12-17, release date: 2008-09-23, Last modification date: 2021-10-20)

Primary citation

Pentelute, B.L.,Gates, Z.P.,Tereshko, V.,Dashnau, J.L.,Vanderkooi, J.M.,Kossiakoff, A.A.,Kent, S.B.
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers
J.Am.Chem.Soc., 130:9695-9701, 2008

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 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.

PubMed: 18598029
DOI: 10.1021/ja8013538

Experimental method

X-RAY DIFFRACTION (1.2 Å)