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PDBsum entry 1vhq
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Structural genomics, unknown function
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PDB id
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1vhq
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural analysis of a set of proteins resulting from a bacterial genomics project.
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Authors
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J.Badger,
J.M.Sauder,
J.M.Adams,
S.Antonysamy,
K.Bain,
M.G.Bergseid,
S.G.Buchanan,
M.D.Buchanan,
Y.Batiyenko,
J.A.Christopher,
S.Emtage,
A.Eroshkina,
I.Feil,
E.B.Furlong,
K.S.Gajiwala,
X.Gao,
D.He,
J.Hendle,
A.Huber,
K.Hoda,
P.Kearins,
C.Kissinger,
B.Laubert,
H.A.Lewis,
J.Lin,
K.Loomis,
D.Lorimer,
G.Louie,
M.Maletic,
C.D.Marsh,
I.Miller,
J.Molinari,
H.J.Muller-Dieckmann,
J.M.Newman,
B.W.Noland,
B.Pagarigan,
F.Park,
T.S.Peat,
K.W.Post,
S.Radojicic,
A.Ramos,
R.Romero,
M.E.Rutter,
W.E.Sanderson,
K.D.Schwinn,
J.Tresser,
J.Winhoven,
T.A.Wright,
L.Wu,
J.Xu,
T.J.Harris.
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Ref.
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Proteins, 2005,
60,
787-796.
[DOI no: ]
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PubMed id
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Abstract
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The targets of the Structural GenomiX (SGX) bacterial genomics project were
proteins conserved in multiple prokaryotic organisms with no obvious sequence
homolog in the Protein Data Bank of known structures. The outcome of this work
was 80 structures, covering 60 unique sequences and 49 different genes.
Experimental phase determination from proteins incorporating Se-Met was carried
out for 45 structures with most of the remainder solved by molecular replacement
using members of the experimentally phased set as search models. An automated
tool was developed to deposit these structures in the Protein Data Bank, along
with the associated X-ray diffraction data (including refined experimental
phases) and experimentally confirmed sequences. BLAST comparisons of the SGX
structures with structures that had appeared in the Protein Data Bank over the
intervening 3.5 years since the SGX target list had been compiled identified
homologs for 49 of the 60 unique sequences represented by the SGX structures.
This result indicates that, for bacterial structures that are relatively easy to
express, purify, and crystallize, the structural coverage of gene space is
proceeding rapidly. More distant sequence-structure relationships between the
SGX and PDB structures were investigated using PDB-BLAST and Combinatorial
Extension (CE). Only one structure, SufD, has a truly unique topology compared
to all folds in the PDB.
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Figure 1.
Figure 1. Ribbon diagrams[54] of the eleven structures
described in the Results and Discussion section: (A) monomer
from the dapE structure (1VGY), (B) homodimer from the nudE
structure (1VHG), (C) monomer from the DUS structure (1VHN), (D)
monomer from the ysdC structure, 1VHE, (E) monomer from the frwX
structure, 1VHO, (F) monomer from the perB structure (1VIZ), (G)
monomer from the plsX structure (1VI1), (H) monomer from the
yqgF structure (1VHX), (I) monomer from the yigZ structure
(1VI7), (J) monomer from the YiiM structure (1O65), (K) the
novel sufD structure (1VH4) with the homodimer interface in the
center.
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The above figure is
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
60,
787-796)
copyright 2005.
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