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PDBsum entry 1a3i
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Extracellular matrix
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PDB id
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1a3i
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References listed in PDB file
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Key reference
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Title
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X-Ray crystallographic determination of a collagen-Like peptide with the repeating sequence (pro-Pro-Gly).
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Authors
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R.Z.Kramer,
L.Vitagliano,
J.Bella,
R.Berisio,
L.Mazzarella,
B.Brodsky,
A.Zagari,
H.M.Berman.
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Ref.
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J Mol Biol, 1998,
280,
623-638.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the triple-helical peptide (Pro-Pro-Gly)10 has been
re-determined to obtain a more accurate description for this widely studied
collagen model and to provide a comparison with the recent high-resolution
crystal structure of a collagen-like peptide containing Pro-Hyp-Gly regions.
This structure demonstrated that hydroxyproline participates extensively in a
repetitive hydrogen-bonded assembly between the peptide and the solvent
molecules. Two separate structural studies of the peptide (Pro-Pro-Gly)10 were
performed with different crystallization conditions, data collection
temperatures, and X-ray sources. The polymer-like structure of one
triple-helical repeat of Pro-Pro-Gly has been determined to 2.0 A resolution in
one case and 1.7 A resolution in the other. The solvent structures of the two
peptides were independently determined specifically for validation purposes. The
two structures display a reverse chain trace compared with the original
structure determination. In comparison with the Hyp-containing peptide, the two
Pro-Pro-Gly structures demonstrate very similar molecular conformation and
analogous hydration patterns involving carbonyl groups, but have different
crystal packing. This difference in crystal packing indicates that the
involvement of hydroxyproline in an extended hydration network is critical for
the lateral assembly and supermolecular structure of collagen.
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Figure 5.
Figure 5. Examples of hydration structure in the (a) Gly!Ala structure (b) PPG 1 or PPG 2 and (c) PPG 0 struc-
tures. In (a) and (b) two water molecules are bound to the carbonyl group of the Y position proline residue (WA and
WN) and one water molecule is bound to the glycine carbonyl group (WN). In (a) two additional water molecules are
bound to O
d
of the hydroxyproline residue. Inter- and intrachain water bridges are then formed by interconnecting
water molecules. In general, the water structure of PPG shows repetitive pentagonal-like inter and intrachain bridges
between carbonyl groups. In (c) two water molecules, W1 and W2, are bound to the carbonyl group of the Y position
proline residue. W1 is also bound to the glycine carbonyl group, forming a one water molecule intrachain bridge. W1
and W2 are connected by W3, forming a three water molecule interchain bridge similar to that seen in (a) and (b).
The Figure was generated with MOLSCRIPT (Kraulis, 1991).
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Figure 9.
Figure 9. Comparing model A with model B from initial
molecular replacement. (a) Model A. Presumably, the carbo-
nyl group of the proline residue in the X position should
make a hydrogen bonding contact with the N atom of the
glycine residue in the neighboring chain. Model A displays
``normal'', N(Gly) to O(Pro)X hydrogen bonds in terms of
length and orientation (broken single line). The distance to
the C
a
of the third chain is longer and the orientation is not
as appropriate for a hydrogen bond (broken double line). (b)
Model B. Interchain hydrogen bonding geometry is per-
turbed. In model B, the oxygen atom appears to be some-
what pointed toward the C
a
(broken double line), rather
than toward the N(Gly), and this length is reasonable for a
hydrogen bond while the distance to the N(Gly) becomes
longer (broken single line). (c) The high-symmetry sequence
and quasi-infinite helical nature of Pro-Pro-Gly implies that
an end-to-end rotation of the peptide chain would give ana-
logous models with only the N and C
a
positions transposed.
Parts (a) and (b) of the Figure were generated with MOL-
SCRIPT (Kraulis, 1991).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
280,
623-638)
copyright 1998.
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Headers
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