3A08

Structure of (PPG)4-OOG-(PPG)4, monoclinic, twinned crystal

Summary for 3A08

• Entry DOI: 10.2210/pdb3a08/pdb
• Related: 1X1K 2CUO 2D3F 2D3H
• Descriptor: collagen-like peptide (2 entities in total)
• Functional Keywords: collagen helix, host-guest peptide, structural protein
• Total number of polymer chains: 6
• Total formula weight: 13869.28

Authors

Okuyama, K.,Morimoto, T.,Wu, G.,Noguchi, K.,Mizuno, K.,Bachinger, H.P. (deposition date: 2009-03-06, release date: 2010-01-12, Last modification date: 2023-11-01)

Primary citation

Okuyama, K.,Morimoto, T.,Narita, H.,Kawaguchi, T.,Mizuno, K.,Bachinger, H.P.,Wu, G.,Noguchi, K.
Two crystal modifications of (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4 reveal the puckering preference of Hyp(X) in the Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs in collagen helices.
Acta Crystallogr.,Sect.D, 66:88-96, 2010

PubMed Abstract: Two crystal modifications of a collagen model peptide, (Pro-Pro-Gly)(4)-Hyp-Hyp-Gly-(Pro-Pro-Gly)(4) [where Hyp is (4R,2S)-L-hydroxyproline], showed very similar unit-cell parameters and belonged to the same space group P2(1). Both crystals exhibited pseudo-merohedral twinning. The main difference was in their molecular-packing arrangements. One modification showed pseudo-hexagonal packing, while the other showed pseudo-tetragonal packing. Despite their different packing arrangements, no significant differences were observed in the hydration states of these modifications. The peptide in the pseudo-tetragonal crystal showed a cyclic fluctuation of helical twists with a period of 20 A, while that in the pseudo-hexagonal crystal did not. In these modifications, the puckering conformations of four of the 12 Hyp residues at the X position of the Hyp(X)-Hyp(Y)-Gly sequence were in the opposite conformations to the previous hypothesis that Hyp(X) residues involved in Hyp(X):Hyp(Y) and Hyp(X):Pro(Y) stacking pairs prefer up-puckering and down-puckering conformations, respectively. Detailed investigation of the molecular interactions between Hyp(X) and adjacent molecules revealed that these opposite conformations appeared because the puckering conformation, which follows the hypothesis, is subject to steric hindrance from the adjacent molecule.

PubMed: 20057053
DOI: 10.1107/S0907444909046642

Experimental method

X-RAY DIFFRACTION (1.22 Å)