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PDBsum entry 1s3o
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DNA binding protein
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PDB id
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1s3o
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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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Sequence-Structure mapping errors in the PDB: ob-Fold domains.
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Authors
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C.Venclovas,
K.Ginalski,
C.Kang.
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Ref.
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Protein Sci, 2004,
13,
1594-1602.
[DOI no: ]
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PubMed id
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Abstract
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The Protein Data Bank (PDB) is the single most important repository of
structural data for proteins and other biologically relevant molecules.
Therefore, it is critically important to keep the PDB data, as much as possible,
error-free. In this study, we have analyzed PDB crystal structures possessing
oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated
folds, for the presence of sequence-structure mapping errors. Using energy-based
structure quality assessment coupled with sequence analyses, we have found that
there are at least five OB-structures in the PDB that have regions where
sequences have been incorrectly mapped onto the structure. We have demonstrated
that the combination of these computation techniques is effective not only in
detecting sequence-structure mapping errors, but also in providing guidance to
correct them. Namely, we have used results of computational analysis to direct a
revision of X-ray data for one of the PDB entries containing a fairly
inconspicuous sequence-structure mapping error. The revised structure has been
deposited with the PDB. We suggest use of computational energy assessment and
sequence analysis techniques to facilitate structure determination when homologs
having known structure are available to use as a reference. Such computational
analysis may be useful in either guiding the sequence-structure assignment
process or verifying the sequence mapping within poorly defined regions.
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Figure 1.
Figure 1. An example of a canonical structure of the
OB-fold based on the N-terminal domain of archaeal aspartyl-tRNA
synthetase (1b8a [PDB]
; Schmitt et al. 1998). Five  -strands
(numbered) form a barrel capped with an  -helix.
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Figure 5.
Figure 5. Structure-based sequence alignment between the
two versions of the budding yeast inorganic pyrophosphatase
structure: 1pyp [PDB]
and a high-resolution structure of the same protein (1e9g [PDB]
). Sequence register errors within 1pyp [PDB]
are denoted in bold.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2004,
13,
1594-1602)
copyright 2004.
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