PDBsum entry 1omu

Serine proteinase inhibitor

PDB id: 1omu

Contents

Protein chain

56 a.a. *

* Residue conservation analysis

PDB id:

1omu

Name:

Serine proteinase inhibitor

Title:

Solution structure of ovomucoid (third domain) from domestic turkey (298k, ph 4.1) (nmr, 50 structures) (refined model using network editing analysis)

Structure:

Ovomucoid (third domain). Chain: a. Synonym: omtky3. Engineered: yes

Source:

Meleagris gallopavo. Turkey. Organism_taxid: 9103. Cell_line: bl21. Organ: egg. Cellular_location: egg white. Gene: om3. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

50 models

Authors:

C.G.Hoogstraten,S.Choe,W.M.Westler,J.L.Markley

Key ref:

C.G.Hoogstraten et al. (1995). Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data. Protein Sci, 4, 2289-2299. PubMed id: 8563625 DOI: 10.1002/pro.5560041106

Date:

11-Oct-95 Release date: 08-Mar-96

Protein chain

P68390  (IOVO_MELGA) -  Ovomucoid from Meleagris gallopavo

Seq: 185 a.a.

Struc: 56 a.a.

DOI no: 10.1002/pro.5560041106

Protein Sci 4:2289-2299 (1995)

PubMed id: 8563625

Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data.

C.G.Hoogstraten, S.Choe, W.M.Westler, J.L.Markley.

ABSTRACT

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.

Selected figure(s)

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).

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. T_N, longitudinal relaxation period; SL_x, transverse relaxation period (spin-locked); T_p 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.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1995, 4, 2289-2299) copyright 1995.

Figures were selected by the author.