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- PDB-9bv4: NMR Solution Structure of Excelsatoxin A in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 9bv4
TitleNMR Solution Structure of Excelsatoxin A in DPC micelles
ComponentsExcelsatoxin A
KeywordsTOXIN
Function / homology: / sodium channel regulator activity / defense response / toxin activity / extracellular region / Excelsatoxin A
Function and homology information
Biological speciesDendrocnide excelsa (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSaipriyaa, P.V. / Chin, Y.K. / Mehdi, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: NMR Solution Structure of Excelsatoxin A in DPC micelles.
Authors: Saipriyaa, P.V. / Chin, Y.K. / Mehdi, M.
History
DepositionMay 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Excelsatoxin A / ExTxA


Mass: 3888.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendrocnide excelsa (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DQP3
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-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
181isotropic13D CBCA(CO)NH
171isotropic13D HCACO
161isotropic13D HN(CA)CB
191isotropic13D HNCO
1101isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: micelle
Contents: 300 uM [U-13C; U-15N] ExTxA, 5 % w/v DPC, 25 mM Bis Tris, 5 % v/v D2O, 95% H2O/5% D2O
Details: ExTxA in DPC micelles, with D2O added / Label: 13C 15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMExTxA[U-13C; U-15N]1
5 % w/vDPCnatural abundance1
25 mMBis Trisnatural abundance1
5 % v/vD2Onatural abundance1
Sample conditionsIonic strength: 25 mM / Label: Condition_1 / pH: 6.5 / Pressure: 101325 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOS-NYang Shen and Ad Baxgeometry optimization
Rowland NMR Toolkit (RNMRTK)Rowlandprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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