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- PDB-5kwz: NMR Solution Structure of Designed Peptide NC_cHH_D1 -

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Basic information

Entry
Database: PDB / ID: 5kwz
TitleNMR Solution Structure of Designed Peptide NC_cHH_D1
ComponentsDesigned peptide NC_cHH_D1
KeywordsDE NOVO PROTEIN / designed peptide
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHarvey, P.J. / Craik, D.J.
CitationJournal: Nature / Year: 2016
Title: Accurate de novo design of hyperstable constrained peptides.
Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P. ...Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P.J. / Rocklin, G.J. / Song, Y. / Linsky, T.W. / Watkins, A. / Rettie, S.A. / Xu, X. / Carter, L.P. / Bonneau, R. / Olson, J.M. / Coutsias, E. / Correnti, C.E. / Szyperski, T. / Craik, D.J. / Baker, D.
History
DepositionJul 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed peptide NC_cHH_D1


Theoretical massNumber of molelcules
Total (without water)3,2731
Polymers3,2731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2470 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Designed peptide NC_cHH_D1


Mass: 3272.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
132isotropic12D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
152isotropic12D 1H-13C HSQC
162isotropic12D ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mg/mL design peptide NC_cHH_D1, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21.0 mg/mL design peptide NC_cHH_D1, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mg/mLdesign peptide NC_cHH_D1natural abundance1
1.0 mg/mLdesign peptide NC_cHH_D1natural abundance2
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / pH: 3 / PH err: 0.1 / Pressure: ambient / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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