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- PDB-7od2: NMR structure of the Anemonia erythraea AeTX-K toxin -

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Basic information

Entry
Database: PDB / ID: 7od2
TitleNMR structure of the Anemonia erythraea AeTX-K toxin
ComponentsKappa-actitoxin-Aer3a
KeywordsTOXIN / Sea anemone Kv channel blockers
Function / homologyShKT domain / ShKT domain profile. / nematocyst / potassium channel regulator activity / toxin activity / extracellular region / Kappa-actitoxin-Aer3a
Function and homology information
Biological speciesAnemonia erythraea (sea anemone)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsQasim, A. / Qassem, N. / Chill, J.H.
Funding support Israel, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2017243 Israel
CitationJournal: To Be Published
Title: Structural determination of AeTX-K by NMR
Authors: Qasim, A. / Shaked, H. / Chill, J.H.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-actitoxin-Aer3a


Theoretical massNumber of molelcules
Total (without water)3,9991
Polymers3,9991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 82structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Kappa-actitoxin-Aer3a / Kappa-AITX-Aer3a / AnerK / Potassium channel toxin AETX K


Mass: 3998.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia erythraea (sea anemone) / Plasmid: pET-32a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q0EAE5
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
122isotropic12D 1H-1H TOCSY
133isotropic12D 1H-1H TOCSY
142isotropic12D 1H-1H NOESY
153isotropic12D 1H-1H NOESY
173isotropic12D 1H-1H COSY
183isotropic12D 1H-13C HMQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution17 % [U-99% 2H] D2O, 93 % H2O, 0.01 % sodium azide, 20 mM sodium phosphate, 10 mM sodium chloride, 0.4 mM [U-98% 15N] AeTX-K toxin, 93% H2O/7% D2O15N_AeTX-K15N93% H2O/7% D2O
solution3100 % [U-99% 2H] D2O, 0.01 % sodium azide, 20 mM sodium phosphate, 10 mM sodium chloride, 0.4 mM AeTX-K toxin, 100% D2OAeTX-K_D2Onon-label100% D2O
solution27 % [U-99% 2H] D2O, 93 % H2O, 0.01 % sodium azide, 20 mM sodium phosphate, 10 mM sodium chloride, 0.4 mM AeTX-K toxin, 93% H2O/7% D2OAeTX-K_H2Onon-label93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
7 %D2O[U-99% 2H]1
93 %H2Onatural abundance1
0.01 %sodium azidenatural abundance1
20 mMsodium phosphatenatural abundance1
10 mMsodium chloridenatural abundance1
0.4 mMAeTX-K toxin[U-98% 15N]1
100 %D2O[U-99% 2H]3
0.01 %sodium azidenatural abundance3
20 mMsodium phosphatenatural abundance3
10 mMsodium chloridenatural abundance3
0.4 mMAeTX-K toxinnatural abundance3
7 %D2O[U-99% 2H]2
93 %H2Onatural abundance2
0.01 %sodium azidenatural abundance2
20 mMsodium phosphatenatural abundance2
10 mMsodium chloridenatural abundance2
0.4 mMAeTX-K toxinnatural abundance2
Sample conditionsIonic strength: 46 mM / Label: condition_1 / pH: 5.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX700 / Manufacturer: Bruker / Model: DRX700 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6Bruker Biospinchemical shift assignment
TopSpin3.6Bruker Biospincollection
TopSpin3.6Bruker Biospindata analysis
TopSpin3.6Bruker Biospinpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 82 / Conformers submitted total number: 23

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