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- PDB-2nbc: Resonance assignments and structure determination of poneritoxin,... -

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Database: PDB / ID: 2nbc
TitleResonance assignments and structure determination of poneritoxin, omega-PONTX-Ae1a, from Anochetus emarginatus
KeywordsTOXIN / Ants / Anochetus / Neurotoxin / Disulfide bond / Venom
Specimen sourceAnochetus emarginatus / arthropod
MethodSolution NMR (Torsion angle dynamics)
Model detailslowest energy, model1
AuthorsChin, Y.K.-Y. / Touchard, A. / King, G.F.
CitationBiochim.Biophys.Acta, 2016, 1860, 2553-2562

Biochim.Biophys.Acta, 2016, 1860, 2553-2562 Yorodumi Papers
Isolation and characterization of a structurally unique beta-hairpin venom peptide from the predatory ant Anochetus emarginatus.
Touchard, A. / Brust, A. / Cardoso, F.C. / Chin, Y.K. / Herzig, V. / Jin, A.H. / Dejean, A. / Alewood, P.F. / King, G.F. / Orivel, J. / Escoubas, P.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 3, 2016 / Release: Jan 11, 2017

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Deposited unit
A: poneritoxin

Theoretical massNumber of molelcules
Total (without water)1,7421

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
Number of conformers (submitted / calculated)20 / 30Best stereochemical property judged by Molprobity
RepresentativeModel #1lowest energy


#1: Protein/peptide poneritoxin

Mass: 1742.087 Da / Num. of mol.: 1 / Source: (natural) Anochetus emarginatus / arthropod

Experimental details


ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1622D 1H-13C HSQC

Sample preparation

NMR sample details
Solution IDContentsSolvent system
12 mM omega-PONTX-Ae1a, 2 mM AMINO GROUP, 5 % D2O, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
22 mM omega-PONTX-Ae1a, 2 mM AMINO GROUP, 100 % D2O, 20 mM sodium phosphate, 100% D2O100% D2O
NMR experiment sample
Conc.UnitsComponentSolution ID
20mMsodium phosphate-41
20mMsodium phosphate-82
NMR experiment sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient / Temperature: 298 kelvins / Temperature units: K

NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600


NMR software
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CcpNmr_AnalysisCCPNpeak picking
CcpNmr_AnalysisCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angle prediction
NMR refineMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Best stereochemical property judged by Molprobity
Conformers calculated total number: 30 / Conformers submitted total number: 20

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