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- PDB-6vh8: NMR Solution Structure of Excelsatoxin A -

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Basic information

Entry
Database: PDB / ID: 6vh8
TitleNMR Solution Structure of Excelsatoxin A
ComponentsExcelsatoxin A
KeywordsTOXIN / ICK peptide / inhibitor cystine knot / plant toxin
Biological speciesDendrocnide excelsa (plant)
MethodSOLUTION NMR / simulated annealing
AuthorsHarvey, P.J. / Durek, T. / Craik, D.J.
CitationJournal: Sci Adv / Year: 2020
Title: Neurotoxic peptides from the venom of the giant Australian stinging tree.
Authors: Gilding, E.K. / Jami, S. / Deuis, J.R. / Israel, M.R. / Harvey, P.J. / Poth, A.G. / Rehm, F.B.H. / Stow, J.L. / Robinson, S.D. / Yap, K. / Brown, D.L. / Hamilton, B.R. / Andersson, D. / ...Authors: Gilding, E.K. / Jami, S. / Deuis, J.R. / Israel, M.R. / Harvey, P.J. / Poth, A.G. / Rehm, F.B.H. / Stow, J.L. / Robinson, S.D. / Yap, K. / Brown, D.L. / Hamilton, B.R. / Andersson, D. / Craik, D.J. / Vetter, I. / Durek, T.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Excelsatoxin A


Theoretical massNumber of molelcules
Total (without water)3,8891
Polymers3,8891
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Excelsatoxin A


Mass: 3888.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Dendrocnide excelsa (plant)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H TOCSY
121isotropic22D 1H-1H NOESY
132isotropic12D 1H-1H ECOSY
142isotropic12D 1H-1H TOCSY
151isotropic12D 1H-15N HSQC
162isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM peptide, 70% H2O/30% CD3CNsample_170% H2O/30% CD3CN
solution21 mM peptide, 70% D2O/30% CD3CNsample_270% D2O/30% CD3CN
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMpeptidenatural abundance1
1 mMpeptidenatural abundance2
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 3.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE NEOBrukerAVANCE NEO9002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
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 lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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