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- PDB-1le0: NMR structure of Tryptophan Zipper 1: a stable, monomeric beta-ha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1le0 | |||||||||
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Title | NMR structure of Tryptophan Zipper 1: a stable, monomeric beta-hairpin with a type II' turn | |||||||||
![]() | Tryptophan Zipper 1 | |||||||||
![]() | DE NOVO PROTEIN / beta-hairpin / type II' turn | |||||||||
Method | SOLUTION NMR / Hybrid distance geometry, simulated annealing using the program DGII, restrained molecular dynamics using the program AMBER, in conjunction with not only distance, dihedral angle restraints, but also 1H chemical shift-based restraints. | |||||||||
![]() | Cochran, A.G. / Skelton, N.J. / Starovasnik, M.A. | |||||||||
![]() | ![]() Title: Tryptophan zippers: stable, monomeric beta -hairpins. Authors: Cochran, A.G. / Skelton, N.J. / Starovasnik, M.A. #1: ![]() Title: Chemical-shift-based methods for structure validation and refinement: Application to tryptophan zipper beta-hairpin peptides Authors: Skelton, N.J. / Cochran, A.G. / Starovasnik, M.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77 KB | Display | ![]() |
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PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 330.7 KB | Display | ![]() |
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Full document | ![]() | 425.8 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1608.776 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence was designed based on experimental data obtained from a model system. The peptide was chemically synthesized and does not appear to occur in nature. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure of trpzip1 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle ...Text: The structure of trpzip1 was originally determined using standard 2D homonuclear techniques (Cochran et al., 2001, Proc. Natl. Acad. Sci. USA, 98, 5578-5583). Distance and dihedral angle restraints were derived from analysis of NOESY, ROESY, DQF-COSY, and COSY-35 data. Chi-1 rotamers and stereospecific assignments for beta-methylene groups were based on combined analysis of 3JHaHb and local ROEs, suggesting that all four Trp residues adopt a chi1 of -60 deg. Quantitative analysis of the 1H chemical shifts, however, revealed that the frequencies of the Hb and He3 resonances of Trp4 and Trp11 were inconsistent with a -60 deg chi1 value, and indicated that the side chains for these tryptophans actually reside primarily in the 180 deg chi1 rotamer (Skelton et al., manuscript in preparation). The current coordinates result from refinement with the Sander module of AMBER (v6.0), and included not only NOE-derived distance restraints and dihedral angle restraints, but also 1H chemical shift-based restraints. Thus, the resulting updated coordinates differ from the previous ones in the side chain orientations of Trp4 and Trp11. However, the rest of the structure is very similar with a backbone rmsd between the average coordinates of the two ensembles of 0.51 angstrom(res.2-11). The two strands are highly twisted, as described previously, but each pair of cross-strand tryptophan rings now show edge-to-face packing against one another. |
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Sample preparation
Details | Contents: 1mM trpzip1 / Solvent system: 92% H2O, 8% D2O, pH 5.5, 0.1mM DSS |
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Sample conditions | Ionic strength: 0 / pH: 5.5 / Pressure: ambient / Temperature: 288 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: Hybrid distance geometry, simulated annealing using the program DGII, restrained molecular dynamics using the program AMBER, in conjunction with not only distance, dihedral angle restraints, ...Method: Hybrid distance geometry, simulated annealing using the program DGII, restrained molecular dynamics using the program AMBER, in conjunction with not only distance, dihedral angle restraints, but also 1H chemical shift-based restraints. Software ordinal: 1 Details: Structures are based on a total of 93 (including 31 intra-residue, 16 sequential, 9 medium-range, and 37 long-range) NOE-derived distance restraints, 15 dihedral angle restraints, and 1H ...Details: Structures are based on a total of 93 (including 31 intra-residue, 16 sequential, 9 medium-range, and 37 long-range) NOE-derived distance restraints, 15 dihedral angle restraints, and 1H chemical shift restraints for 39 carbon-bound 1H resonances; (chemical shift restraints were not imposed for the terminal residues, or for side chains exhibiting evidence of rotational averaging). The ensemble agrees well with the experimental restraints with no distance or dihedral angle violations greater than 0.10 angstrom or 5 deg, respectively, and an average rmsd of only 0.091 ppm between observed and calculated chemical shifts. | ||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 90 / Conformers submitted total number: 20 |