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- PDB-1j4m: Minimized average structure of the 14-residue peptide RG-KWTY-NG-... -

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Basic information

Entry
Database: PDB / ID: 1j4m
TitleMinimized average structure 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 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)1 / -
Representative

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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: 5.0 / Pressure: ambient / Temperature: 283 K

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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: Energy minimisation of the mean structure was done with the GROMOS96 implementation of Swiss-PdbViewer.
NMR ensembleConformers submitted total number: 1

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