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- PDB-2dx4: NMR structure of DP5_conformation2: monomeric beta-hairpin -

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Entry
Database: PDB / ID: 2dx4
TitleNMR structure of DP5_conformation2: monomeric beta-hairpin
ComponentsDP5_conformation2
KeywordsDE NOVO PROTEIN / beta-hairpin
MethodSOLUTION NMR / distance geometry
AuthorsTamura, A. / Araki, M.
CitationJournal: Proteins / Year: 2006
Title: Transformation of an alpha-helix peptide into a beta-hairpin induced by addition of a fragment results in creation of a coexisting state.
Authors: Araki, M. / Tamura, A.
History
DepositionAug 23, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 2024Group: 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: DP5_conformation2


Theoretical massNumber of molelcules
Total (without water)2,1171
Polymers2,1171
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide DP5_conformation2


Mass: 2117.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized and does not appear to occur in nature. This sequence was designed based on a strategy.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
NMR detailsText: This structures were determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 1mM TP; 10mM acetic acid-3mM NAOH buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 6.5mM / pH: 4.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
NMRPipe1.7processing
XwinNMR1.3processing
DYANA1.5refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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