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- PDB-1jy9: MINIMIZED AVERAGE STRUCTURE OF DP-TT2 -

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Entry
Database: PDB / ID: 1jy9
TitleMINIMIZED AVERAGE STRUCTURE OF DP-TT2
ComponentsDP-TT2
KeywordsDE NOVO PROTEIN / beta-hairpin
MethodSOLUTION NMR / NOE intensities were qualitatively assigned to be strong, medium, weak or very weak, and assigned constraints of 3, 4, 5, and 6 respectively; a total of 32 restraints were used for DP-TT2. Restraints were checked using "distance check" function within DYANA which showed there were no "lonely" or possibly misassigned NOEs which could unduly influence the final conformation. DYANA was used to generate 500 random structures, which were subsequently annealed. The best 10 structures (fewest restraint violations) were selected. This entry contains the minimized average structure.
AuthorsStanger, H.E. / Syud, F.A. / Espinosa, J.F. / Giriat, I. / Muir, T. / Gellman, S.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Length-dependent stability and strand length limits in antiparallel beta -sheet secondary structure.
Authors: Stanger, H.E. / Syud, F.A. / Espinosa, J.F. / Giriat, I. / Muir, T. / Gellman, S.H.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond / pdbx_entry_details
Remark 999SEQUENCE RESIDUE 12 IN THE PEPTIDE IS ORNITHINE. FOR MODELLING, LYSINE WAS USED IN PLACE OF ...SEQUENCE RESIDUE 12 IN THE PEPTIDE IS ORNITHINE. FOR MODELLING, LYSINE WAS USED IN PLACE OF ORNITHINE FOR EASE OF CALCULATION.

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Structure visualization

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Assembly

Deposited unit
A: DP-TT2


Theoretical massNumber of molelcules
Total (without water)2,2421
Polymers2,2421
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 DP-TT2


Mass: 2241.559 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized by solid phase peptide synthesis.
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: ROESY to check for spin diffusion.

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Sample preparation

DetailsContents: 1 mM peptide / Solvent system: 9:1 H2O:D2O, 100 mM Acetic Acid
Sample conditionspH: 3.8 / Pressure: ambient / Temperature: 277 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DIANA1.5Guntert, Mumenthaler, Wuthrichstructure solution
DIANA1.5Guntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: NOE intensities were qualitatively assigned to be strong, medium, weak or very weak, and assigned constraints of 3, 4, 5, and 6 respectively; a total of 32 restraints were used for DP-TT2. ...Method: NOE intensities were qualitatively assigned to be strong, medium, weak or very weak, and assigned constraints of 3, 4, 5, and 6 respectively; a total of 32 restraints were used for DP-TT2. Restraints were checked using "distance check" function within DYANA which showed there were no "lonely" or possibly misassigned NOEs which could unduly influence the final conformation. DYANA was used to generate 500 random structures, which were subsequently annealed. The best 10 structures (fewest restraint violations) were selected. This entry contains the minimized average structure.
Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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