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- PDB-2i9m: Design of a-helix based on conformationally restricted libraries -

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Basic information

Entry
Database: PDB / ID: 2i9m
TitleDesign of a-helix based on conformationally restricted libraries
ComponentsMHA6
KeywordsDE NOVO PROTEIN / HELIX
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPantoja-Uceda, D. / Pineda-Lucena, A.
CitationJournal: To be Published
Title: Design of minimal independent protein motifs able to fold autonomously
Authors: Pantoja-Uceda, D. / Pastor, M.T. / Salgado, J. / Pineda-Lucena, A. / Perez-Paya, E.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: MHA6


Theoretical massNumber of molelcules
Total (without water)1,7411
Polymers1,7411
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein/peptide MHA6


Mass: 1740.998 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the designed peptide was 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 TOCSY
1212D NOESY
1322D NOESY
1422D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM MHA6, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM MHA6, 100% D2O100% D2O
Sample conditionspH: 5 / 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 AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guentertstructure solution
NMRView5.0.4Johnsondata analysis
CYANA2.1Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 171 NOE-derived distance constraints.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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