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- PDB-1k43: 10 Structure Ensemble of the 14-residue peptide RG-KWTY-NG-ITYE-G... -

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Basic information

Entry
Database: PDB / ID: 1k43
Title10 Structure Ensemble of the 14-residue peptide RG-KWTY-NG-ITYE-GR (MBH12)
ComponentsMBH12
KeywordsDE NOVO PROTEIN / beta-hairpin
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics (DYANA)
AuthorsPastor, M.T. / Lopez de la Paz, M. / Lacroix, E. / Serrano, L. / Perez-Paya, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Combinatorial approaches: a new tool to search for highly structured beta-hairpin peptides.
Authors: Pastor, M.T. / Lopez de la Paz, M. / Lacroix, E. / Serrano, L. / Perez-Paya, E.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: MBH12


Theoretical massNumber of molelcules
Total (without water)1,7041
Polymers1,7041
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)10 / 50structures with the lowest energy
RepresentativeModel #6lower rmsd with respect to mean

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Components

#1: Protein/peptide MBH12


Mass: 1703.877 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized using Fmoc chemistry.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D ROESY
1222D NOESY
1332D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Peptide MBH1290% H2O/10% D2O
21 mM Peptide MBH12100% D2O
31 mM Peptide MBH1240% CD3OD, 60% H2O
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 283 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
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerdata analysis
DYANA1.5Guntert, P. et al.structure solution
GROMOS96van Gunsterenrefinement
RefinementMethod: simulated annealing, torsion angle dynamics (DYANA) / Software ordinal: 1
Details: The structures are based on a total of 70 restraints, 60 are NOE-derived distance constraints and 10 dihedral angle restraints. The pairwise RMSD for residues 3-12 was 0.38 +/- 0.21 A for ...Details: The structures are based on a total of 70 restraints, 60 are NOE-derived distance constraints and 10 dihedral angle restraints. The pairwise RMSD for residues 3-12 was 0.38 +/- 0.21 A for the backbone and 1.36 +/- 0.35 A for all heavy atoms. The estimated beta-hairpin population of this peptide is 66 +/- 4%. The first and last two residues (RG) are disordered, because they were added just to avoid aggregation. The side chains of Trp4, Tyr6, Ile9 and Tyr11 are interacting in one side of the beta hairpin, forming a hydrophobic cluster. Asn7 at position L1 of the beta-turn is directed outwards from the beta-hairpin, as expected for a type I' beta-turn.
NMR representativeSelection criteria: lower rmsd with respect to mean
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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