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PDBsum entry 3al1
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Structural protein
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PDB id
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3al1
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PDB id:
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Structural protein
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Title:
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Designed peptide alpha-1, racemic p1bar form
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Structure:
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Protein (d, l-alpha-1). Chain: a, b. Engineered: yes. Other_details: n termini are acetylated
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Source:
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Synthetic: yes. Other_details: peptide was synthesized via solid phase synthesis and designed to be an amphiphilic helix
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Resolution:
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0.75Å
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R-factor:
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0.131
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R-free:
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0.145
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Authors:
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W.R.Patterson,D.H.Anderson,W.F.Degrado,D.Cascio,D.Eisenberg
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Key ref:
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W.R.Patterson
et al.
(1999).
Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
Protein Sci,
8,
1410-1422.
PubMed id:
DOI:
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Date:
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26-Oct-98
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Release date:
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04-Nov-98
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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DOI no:
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Protein Sci
8:1410-1422
(1999)
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PubMed id:
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Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
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W.R.Patterson,
D.H.Anderson,
W.F.DeGrado,
D.Cascio,
D.Eisenberg.
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ABSTRACT
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We report the 0.75 A crystal structure of a racemic mixture of the 12-residue
designed peptide "Alpha-1" (Acetyl-ELLKKLLEELKG), the L-enantiomer of which is
described in the accompanying paper. Equivalent solutions of the centrosymmetric
bilayers were determined by two direct phasing programs in space groups P1 and
P1bar. The unit cell contains two L-alpha-helices and two D-alpha-helices. The
columnar-sheet bilayer motif seen in L-Alpha-1 is maintained in the D,L-Alpha-1
structure except that each sheet of head-to-tail helices is composed of one
enantiomer and is related to its neighboring sheets by inversion symmetry.
Comparison to the L-Alpha-1 structure provides further insight into peptide
design. The high resolution and small asymmetric unit allowed building an
intricate model (R = 13.1%, Rfree = 14.5%) that incorporates much of the
discrete disorder of peptide and solvent. Ethanolamine and
2-methyl-2,4-pentanediol (MPD) molecules bind near helix termini. Rigid body
analysis identifies sites of restricted displacements and torsions. Side-chain
discrete disorder propagates into the backbone of one helix but not the other.
Although no side chain in Alpha-1 is rigid, the environments in the crystal
restrict some of them to no or only one active torsion.
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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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J.R.Banigan,
K.Mandal,
M.R.Sawaya,
V.Thammavongsa,
A.P.Hendrickx,
O.Schneewind,
T.O.Yeates,
and
S.B.Kent
(2010).
Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.
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Protein Sci,
19,
1840-1849.
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PDB code:
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K.Mandal,
B.L.Pentelute,
V.Tereshko,
A.A.Kossiakoff,
and
S.B.Kent
(2009).
X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods.
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J Am Chem Soc,
131,
1362-1363.
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PDB code:
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K.Mandal,
B.L.Pentelute,
V.Tereshko,
V.Thammavongsa,
O.Schneewind,
A.A.Kossiakoff,
and
S.B.Kent
(2009).
Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods.
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Protein Sci,
18,
1146-1154.
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PDB codes:
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B.L.Pentelute,
Z.P.Gates,
V.Tereshko,
J.L.Dashnau,
J.M.Vanderkooi,
A.A.Kossiakoff,
and
S.B.Kent
(2008).
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers.
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J Am Chem Soc,
130,
9695-9701.
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PDB codes:
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J.Wang,
M.Dauter,
R.Alkire,
A.Joachimiak,
and
Z.Dauter
(2007).
Triclinic lysozyme at 0.65 A resolution.
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Acta Crystallogr D Biol Crystallogr,
63,
1254-1268.
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PDB code:
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M.Jaskolski,
M.Gilski,
Z.Dauter,
and
A.Wlodawer
(2007).
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
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Acta Crystallogr D Biol Crystallogr,
63,
611-620.
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Y.E.Kitaev,
A.G.Panfilov,
V.P.Smirnov,
and
P.Tronc
(2003).
Why biomolecules prefer only a few crystal structures.
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Phys Rev E Stat Nonlin Soft Matter Phys,
67,
011907.
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N.Matsugaki,
and
M.Shiono
(2001).
Ab initio structure determinations by direct-space methods: tests of low-density elimination.
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Acta Crystallogr D Biol Crystallogr,
57,
95.
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G.G.Privé,
D.H.Anderson,
L.Wesson,
D.Cascio,
and
D.Eisenberg
(1999).
Packed protein bilayers in the 0.90 A resolution structure of a designed alpha helical bundle.
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Protein Sci,
8,
1400-1409.
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PDB code:
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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
code is
shown on the right.
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Links
