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PDBsum entry 1v4f
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Structural protein
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PDB id
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1v4f
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PDB id:
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Structural protein
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Title:
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Crystal structures of collagen model peptides with pro-hyp-gly sequence at 1.3a
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Structure:
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Collagen like peptide. Chain: a. Engineered: yes. Collagen like peptide. Chain: b. Engineered: yes. Collagen like peptide. Chain: c. Engineered: yes
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Source:
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Synthetic: yes. Other_details: this triplet is very popular in the collagen sequence.. Sequence.
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Resolution:
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1.26Å
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R-factor:
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0.133
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R-free:
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0.159
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Authors:
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K.Okuyama,C.Hongo,R.Fukushima,G.Wu,K.Noguchi,Y.Tanaka,N.Nishino
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Key ref:
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K.Okuyama
et al.
(2004).
Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering.
Biopolymers,
76,
367-377.
PubMed id:
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Date:
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13-Nov-03
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Release date:
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03-Aug-04
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Headers
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References
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Biopolymers
76:367-377
(2004)
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PubMed id:
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Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering.
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K.Okuyama,
C.Hongo,
R.Fukushima,
G.Wu,
H.Narita,
K.Noguchi,
Y.Tanaka,
N.Nishino.
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ABSTRACT
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Triple-helical structures of (Pro-Hyp-Gly)n (n = 10, 11) at 100 K and room
temperature (RT) were analyzed at 1.26 A resolution by using synchrotron
radiation data. Totals of 49 and 42 water molecules per seven triplets in an
asymmetric unit were found for the structures at 100 K and RT, respectively.
These water molecules were classified into two groups, those in the first and
second hydration shells. Although there was no significant difference between
water molecules in the first shell at 100 K and those at RT, a significant
difference between those in the second shell was observed. That is, the number
of water molecules at RT decreased to one half and the average distance from
peptide chains at RT became longer by about 0.3 A. On the other hand, of seven
triplets in an asymmetric unit, three proline residues at the X position at 100
K clearly showed an up-puckering conformation, as opposed to the recent
propensity-based hypothesis for the stabilization and destabilization of
triple-helical structures by proline hydroxylation. This puckering was
attributed to the interaction between proline rings and the surrounding water
molecules at 100 K, which is much weaker at RT, as shown by longer average
distance from peptide chains.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.Vitagliano,
R.Berisio,
and
A.De Simone
(2011).
Role of hydration in collagen recognition by bacterial adhesins.
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Biophys J,
100,
2253-2261.
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K.Mizuno,
and
H.P.Bächinger
(2010).
The effect of deuterium oxide on the stability of the collagen model peptides H-(Pro-Pro-Gly)(10)-OH, H-(Gly-Pro-4(R)Hyp)(9)-OH, and Type I collagen.
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Biopolymers,
93,
93.
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K.Okuyama,
T.Morimoto,
H.Narita,
T.Kawaguchi,
K.Mizuno,
H.P.Bächinger,
G.Wu,
and
K.Noguchi
(2010).
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.
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Acta Crystallogr D Biol Crystallogr,
66,
88-96.
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PDB codes:
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M.D.Shoulders,
K.A.Satyshur,
K.T.Forest,
and
R.T.Raines
(2010).
Stereoelectronic and steric effects in side chains preorganize a protein main chain.
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Proc Natl Acad Sci U S A,
107,
559-564.
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PDB code:
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K.Okuyama,
C.Hongo,
G.Wu,
K.Mizuno,
K.Noguchi,
S.Ebisuzaki,
Y.Tanaka,
N.Nishino,
and
H.P.Bächinger
(2009).
High-resolution structures of collagen-like peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4)]: Implications for triple-helix hydration and Hyp(X) puckering.
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Biopolymers,
91,
361-372.
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PDB codes:
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M.K.Koski,
R.Hieta,
M.Hirsilä,
A.Rönkä,
J.Myllyharju,
and
R.K.Wierenga
(2009).
The crystal structure of an algal prolyl 4-hydroxylase complexed with a proline-rich peptide reveals a novel buried tripeptide binding motif.
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J Biol Chem,
284,
25290-25301.
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PDB code:
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A.Zavalin,
D.L.Hachey,
M.Sundaramoorthy,
S.Banerjee,
S.Morgan,
L.Feldman,
N.Tolk,
and
D.W.Piston
(2008).
Kinetics of a collagen-like polypeptide fragmentation after mid-IR free-electron laser ablation.
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Biophys J,
95,
1371-1381.
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J.C.Leo,
H.Elovaara,
B.Brodsky,
M.Skurnik,
and
A.Goldman
(2008).
The Yersinia adhesin YadA binds to a collagenous triple-helical conformation but without sequence specificity.
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Protein Eng Des Sel,
21,
475-484.
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S.P.Boudko,
J.Engel,
K.Okuyama,
K.Mizuno,
H.P.Bächinger,
and
M.A.Schumacher
(2008).
Crystal Structure of Human Type III Collagen Gly991-Gly1032 Cystine Knot-containing Peptide Shows Both 7/2 and 10/3 Triple Helical Symmetries.
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J Biol Chem,
283,
32580-32589.
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PDB code:
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V.K.Pálfi,
and
A.Perczel
(2008).
How stable is a collagen triple helix? An ab initio study on various collagen and beta-sheet forming sequences.
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J Comput Chem,
29,
1374-1386.
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F.H.Lin,
L.A.Graham,
R.L.Campbell,
and
P.L.Davies
(2007).
Structural modeling of snow flea antifreeze protein.
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Biophys J,
92,
1717-1723.
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K.Okuyama,
H.Narita,
T.Kawaguchi,
K.Noguchi,
Y.Tanaka,
and
N.Nishino
(2007).
Unique side chain conformation of a Leu residue in a triple-helical structure.
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Biopolymers,
86,
212-221.
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PDB codes:
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K.Okuyama,
G.Wu,
N.Jiravanichanun,
C.Hongo,
and
K.Noguchi
(2006).
Helical twists of collagen model peptides.
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Biopolymers,
84,
421-432.
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K.Okuyama,
X.Xu,
M.Iguchi,
and
K.Noguchi
(2006).
Revision of collagen molecular structure.
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Biopolymers,
84,
181-191.
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M.A.Schumacher,
K.Mizuno,
and
H.P.Bächinger
(2006).
The crystal structure of a collagen-like polypeptide with 3(S)-hydroxyproline residues in the Xaa position forms a standard 7/2 collagen triple helix.
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J Biol Chem,
281,
27566-27574.
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PDB code:
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M.Crisma,
F.Formaggio,
A.Moretto,
and
C.Toniolo
(2006).
Peptide helices based on alpha-amino acids.
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Biopolymers,
84,
3.
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N.Jiravanichanun,
N.Nishino,
and
K.Okuyama
(2006).
Conformation of alloHyp in the Y position in the host-guest peptide with the pro-pro-gly sequence: implication of the destabilization of (Pro-alloHyp-Gly)10.
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Biopolymers,
81,
225-233.
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M.Schumacher,
K.Mizuno,
and
H.P.Bächinger
(2005).
The crystal structure of the collagen-like polypeptide (glycyl-4(R)-hydroxyprolyl-4(R)-hydroxyprolyl)9 at 1.55 A resolution shows up-puckering of the proline ring in the Xaa position.
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J Biol Chem,
280,
20397-20403.
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PDB code:
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N.Jiravanichanun,
C.Hongo,
G.Wu,
K.Noguchi,
K.Okuyama,
N.Nishino,
and
T.Silva
(2005).
Unexpected puckering of hydroxyproline in the guest triplets, hyp-pro-gly and pro-allohyp-gly sandwiched between pro-pro-gly sequence.
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Chembiochem,
6,
1184-1187.
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PDB code:
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T.Koide
(2005).
Triple helical collagen-like peptides: engineering and applications in matrix biology.
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Connect Tissue Res,
46,
131-141.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
