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- PDB-7rfa: NMR Solution structure of linear [T20K]kalataB1 -

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Basic information

Entry
Database: PDB / ID: 7rfa
TitleNMR Solution structure of linear [T20K]kalataB1
ComponentsKalata-B4
KeywordsBIOSYNTHETIC PROTEIN / peptide cyclotide / linear peptide acyclotide
Function / homologyCyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Kalata-B4
Function and homology information
Biological speciesOldenlandia affinis (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Craik, D.J. / Gruber, C.W.
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Importance of the Cyclic Cystine Knot Structural Motif for Immunosuppressive Effects of Cyclotides.
Authors: Hellinger, R. / Muratspahic, E. / Devi, S. / Koehbach, J. / Vasileva, M. / Harvey, P.J. / Craik, D.J. / Grundemann, C. / Gruber, C.W.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kalata-B4


Theoretical massNumber of molelcules
Total (without water)2,9451
Polymers2,9451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Kalata-B4


Mass: 2945.421 Da / Num. of mol.: 1 / Mutation: T20K / Source method: obtained synthetically / Source: (synth.) Oldenlandia affinis (plant) / References: UniProt: P83938

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TOCSY
121isotropic12D NOESY
131isotropic12D 1H-15N HSQC
142isotropic12D TOCSY
152isotropic12D 1H-13C HSQC aliphatic
162isotropic12D 1H-1H ECOSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM peptide, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21.0 mM peptide, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMpeptidenatural abundance1
1.0 mMpeptidenatural abundance2
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / pH: 3.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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