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PDBsum entry 1omt
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Serine proteinase inhibitor
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PDB id
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1omt
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References listed in PDB file
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Key reference
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Title
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Comparison of the accuracy of protein solution structures derived from conventional and network-Edited noesy data.
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Authors
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C.G.Hoogstraten,
S.Choe,
W.M.Westler,
J.L.Markley.
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Ref.
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Protein Sci, 1995,
4,
2289-2299.
[DOI no: ]
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PubMed id
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Abstract
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Network-editing experiments are variants of the basic NOESY experiment that
allow more accurate direct measurement of interproton distances in
macromolecules by defeating specific spin-diffusion pathways. Two
network-editing approaches, block-decoupled NOESY and
complementary-block-decoupled-NOESY, were applied as three-dimensional,
heteronuclear-edited experiments to distance measurement in a small protein,
turkey ovomucoid third domain (OMTKY3). Two-hundred and twelve of the original
655 distance constraints observed in this molecule (Krezel AM et al., 1994, J
Mol Biol 242:203-214) were improved by their replacement by distances derived
from network-edited spectra, and distance geometry/simulated annealing solution
structure calculations were performed from both the unimproved and improved
distance sets. The resulting two families of structures were found to differ
significantly, the most important differences being the hinge angle of a
beta-turn and an expansion of the sampled conformation space in the region of
the reactive-site loop. The structures calculated from network-editing data are
interpreted as a more accurate model of the solution conformation of OMTKY3.
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Figure 5.
Fig. 5. Average structures of OMTKY3. Comparison of polypeptide
backbone for residues 7-56 of unminimized average structures calculated
from crude (blue) and improved (red) data. For calculation of average
structures, structures within a set were superimposed by reference
to the backbone atoms for residues 7-56; the two average structures were
superimposed in the same way for comparison. Widths of the ribbons
are proportional to the backbone pairwise RMSD for the appropriate
set of structures. Figure prepared using INSIGHT-II 2.3.5 software
package (Biosym Technologies, Inc., San Diego, California).
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Figure 7.
Fig. 7. hree-dimcnsionalnetwork-editig pulse sequences. NMR pulse
Three-dimensional network-editing pulse sequences. NMR pulse
sequences for the BD-NOESY-HSQC (A) and CBD-NOESY-HSQC (B)
experiments. Upper portion shows the 1H RF pulses, 15N RF pulses,
and z-gradient pulses for the framework NOESY-HSQC sequence; network-
editing mixing sequences are indicated separately (A, BD-NOESY;
B, CBD-NOESY). Shaded triangles for RF pulses indicate low-power
selective pulses. Diagonal shading indicates spin lock. TN, longitudinal
relaxation period; SLx, transverse relaxation period (spin-locked); Tp
precession delay; Delta, 1/4J delay for evolution of heteronuclear coupling.
Phase cycle: psi1: 0, pi ; psi2: 0, 0, pi , pi; receiver: 0, pi , pi, 0.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1995,
4,
2289-2299)
copyright 1995.
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Secondary reference #1
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Title
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Solution structure of turkey ovomucoid third domain as determined from nuclear magnetic resonance data.
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Authors
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A.M.Krezel,
P.Darba,
A.D.Robertson,
J.Fejzo,
S.Macura,
J.L.Markley.
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Ref.
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J Mol Biol, 1994,
242,
203-214.
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PubMed id
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