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Open data
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Basic information
Entry | Database: PDB / ID: 1n09 | ||||||
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Title | A minimal beta-hairpin peptide scaffold for beta-turn display | ||||||
![]() | bhpW, disulfide cyclized beta-hairpin peptide | ||||||
![]() | DE NOVO PROTEIN / beta hairpin / beta turn / cyclic disulfide | ||||||
Method | SOLUTION NMR / Distance geometry, restrained molecular dynamics with chemical shift restraints. | ||||||
![]() | Russell, S.J. / Blandl, T. / Skelton, N.J. / Cochran, A.G. | ||||||
![]() | ![]() Title: Stability of cyclic beta-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair Authors: Russell, S.J. / Blandl, T. / Skelton, N.J. / Cochran, A.G. #1: ![]() Title: A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins Authors: Cochran, A.G. / Tong, R.T. / Starovasnik, M.A. / Park, E.J. / McDowell, R.S. / Theaker, J.E. / Skelton, N.J. | ||||||
History |
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Remark 999 | SEQUENCE There is no sequence database reference since the peptide is a de novo designed sequence. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.9 KB | Display | ![]() |
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PDB format | ![]() | 43.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 333.3 KB | Display | ![]() |
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Full document | ![]() | 422.3 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 7.7 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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1 |
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1179.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Chemical shift assignments were determined using standard 2D homonuclear techniques. |
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Sample preparation
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Sample conditions |
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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 | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | Method: Distance geometry, restrained molecular dynamics with chemical shift restraints. Software ordinal: 1 Details: 100 structures were calculated using distance geometry. The 80 structures of lowest penalty function were refined using the Sander module of AMBER (v6.0). The calculation employed 79 ...Details: 100 structures were calculated using distance geometry. The 80 structures of lowest penalty function were refined using the Sander module of AMBER (v6.0). The calculation employed 79 distance restraints, 12 dihedral angle restraints and 13 chemical shift restraints. The 20 structures of lowest violation energy were chosen to represent the structure. There are no violations of the input restraints > 0.1 A or 2 degrees. The rms. difference between calculation and observed chemical shifts is 0.09 ppm. 79% of the backbone geometries are in the most favourable region of the Ramachandran plot. The backbone heavy atom rmsd from the mean structure is 0.39+/-0.08 A. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 80 / Conformers submitted total number: 20 |