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- PDB-1n09: A minimal beta-hairpin peptide scaffold for beta-turn display -

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Basic information

Entry
Database: PDB / ID: 1n09
TitleA minimal beta-hairpin peptide scaffold for beta-turn display
ComponentsbhpW, disulfide cyclized beta-hairpin peptide
KeywordsDE NOVO PROTEIN / beta hairpin / beta turn / cyclic disulfide
MethodSOLUTION NMR / Distance geometry, restrained molecular dynamics with chemical shift restraints.
AuthorsRussell, S.J. / Blandl, T. / Skelton, N.J. / Cochran, A.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 2003
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: Journal: J.Am.Chem.Soc. / Year: 2001
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
DepositionOct 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE There is no sequence database reference since the peptide is a de novo designed sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: bhpW, disulfide cyclized beta-hairpin peptide


Theoretical massNumber of molelcules
Total (without water)1,1791
Polymers1,1791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80structures with the least restraint violations
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide bhpW, disulfide cyclized beta-hairpin peptide


Mass: 1179.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D ROESY
2422D ROESY
2522D COSY-35
NMR detailsText: Chemical shift assignments were determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM peptide, unbuffered at pH 5.090% H2O/10% D2O
25 mM peptide, unbuffered at pH 5.0100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1051 atm288 K
2051 atm288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1brukercollection
Felix980brukerdata analysis
DGII980Tim Havelstructure solution
Amber6Case, Kollman, ET. AL.refinement
Amber6.Ostructure solution
RefinementMethod: 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 representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 80 / Conformers submitted total number: 20

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