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- PDB-7kpd: NMR Solution Structure of Acyclotide ribe 31 -

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Basic information

Entry
Database: PDB / ID: 7kpd
TitleNMR Solution Structure of Acyclotide ribe 31
ComponentsAcyclotide ribe 31
KeywordsANTIMICROBIAL PROTEIN
Biological speciesRinorea bengalensis (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Craik, D.J. / Dang, T.T.
CitationJournal: J.Nat.Prod. / Year: 2021
Title: In Planta Discovery and Chemical Synthesis of Bracelet Cystine Knot Peptides from Rinorea bengalensis .
Authors: Dang, T.T. / Chan, L.Y. / Tombling, B.J. / Harvey, P.J. / Gilding, E.K. / Craik, D.J.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 20, 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:
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Assembly

Deposited unit
A: Acyclotide ribe 31


Theoretical massNumber of molelcules
Total (without water)3,1401
Polymers3,1401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Acyclotide ribe 31


Mass: 3139.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rinorea bengalensis (plant)
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
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

DetailsType: solution / Contents: 1.0 mM ribe 31, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: ribe 31 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: nd Not defined / Label: conditions_1 / pH: 4 / 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: 100 / Conformers submitted total number: 20

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