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PDBsum entry 2dcq
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Unknown function
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PDB id
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2dcq
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References listed in PDB file
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Key reference
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Title
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Automated protein structure determination from nmr spectra.
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Authors
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B.López-Méndez,
P.Güntert.
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Ref.
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J Am Chem Soc, 2006,
128,
13112-13122.
[DOI no: ]
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PubMed id
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Abstract
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Fully automated structure determination of proteins in solution (FLYA) yields,
without human intervention, three-dimensional protein structures starting from a
set of multidimensional NMR spectra. Integrating existing and new software,
automated peak picking over all spectra is followed by peak list filtering, the
generation of an ensemble of initial chemical shift assignments, the
determination of consensus chemical shift assignments for all (1)H, (13)C, and
(15)N nuclei, the assignment of NOESY cross-peaks, the generation of distance
restraints, and the calculation of the three-dimensional structure by torsion
angle dynamics. The resulting, preliminary structure serves as additional input
to the second stage of the procedure, in which a new ensemble of chemical shift
assignments and a refined structure are calculated. The three-dimensional
structures of three 12-16 kDa proteins computed with the FLYA algorithm
coincided closely with the conventionally determined structures. Deviations were
below 0.95 A for the backbone atom positions, excluding the flexible chain
termini. 96-97% of all backbone and side-chain chemical shifts in the structured
regions were assigned to the correct residues. The purely computational FLYA
method is suitable for substituting all manual spectra analysis and thus
overcomes a main efficiency limitation of the NMR method for protein structure
determination.
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Secondary reference #1
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Title
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Solution structure of the rhodanese homology domain at4g01050(175-295) from arabidopsis thaliana.
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Authors
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D.Pantoja-Uceda,
B.López-Méndez,
S.Koshiba,
M.Inoue,
T.Kigawa,
T.Terada,
M.Shirouzu,
A.Tanaka,
M.Seki,
K.Shinozaki,
S.Yokoyama,
P.Güntert.
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Ref.
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Protein Sci, 2005,
14,
224-230.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Structure-based sequence alignment of the
rhodanese and rhodanese homology domains with known structure
according to the program DALI (Holm and Sander 1996). Domain
names are as in Table 2 Go- . The
catalytic position is shown in italics. Residues in helices or
 -strands are
highlighted in green and in cyan, respectively, and  -helices and
-strands are
labeled.
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The above figure is
reproduced from the cited reference
with permission from the Protein Society
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Secondary reference #2
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Title
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Nmr assignment of the hypothetical rhodanese domain at4g01050 from arabidopsis thaliana.
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Authors
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D.Pantoja-Uceda,
B.López-Méndez,
S.Koshiba,
T.Kigawa,
M.Shirouzu,
T.Terada,
M.Inoue,
T.Yabuki,
M.Aoki,
E.Seki,
T.Matsuda,
H.Hirota,
M.Yoshida,
A.Tanaka,
T.Osanai,
M.Seki,
K.Shinozaki,
S.Yokoyama,
P.Güntert.
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Ref.
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J Biomol Nmr, 2004,
29,
207-208.
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PubMed id
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