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- PDB-5wxe: Highly disulfide-constrained antifeedant jasmintides from Jasminu... -

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Basic information

Entry
Database: PDB / ID: 5wxe
TitleHighly disulfide-constrained antifeedant jasmintides from Jasminum sambac flowers
Componentsjasmintide js3
KeywordsUNKNOWN FUNCTION / jasmintide / disulfide-constrained antifeedant / Jasminum sambac
Function / homologyJasmintide js3
Function and homology information
Biological speciesJasminum sambac (Arabian jasmine)
MethodSOLUTION NMR / simulated annealing
AuthorsKumari, G. / Wong, K.H. / Serra, A. / Shin, J. / Yoon, H.S. / Sze, S.K. / James, P.T.
CitationJournal: To Be Published
Title: Highly disulfide-constrained antifeedant jasmintides from Jasminum sambac flowers
Authors: Kumari, G. / Wong, K.H. / Serra, A. / Shin, J. / Yoon, H.S. / Sze, S.K. / James, P.T.
History
DepositionJan 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: jasmintide js3


Theoretical massNumber of molelcules
Total (without water)3,2271
Polymers3,2271
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide jasmintide js3


Mass: 3226.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jasminum sambac (Arabian jasmine) / Production host: Jasminum sambac (Arabian jasmine) / References: UniProt: A0A2R2JFU3*PLUS

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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 DQF-COSY
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM Not labled jasmintide js3, 90% H2O/10% D2Oh2o_sample90% H2O/10% D2O
solution20.7 mM Not labeled jasmintide js3, 100% D2Od2o_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMjasmintide js3Not labled1
0.7 mMjasmintide js3Not labeled2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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