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- PDB-9kk3: Solution structure of kappa-conotoxin RIIIK -

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Basic information

Entry
Database: PDB / ID: 9kk3
TitleSolution structure of kappa-conotoxin RIIIK
ComponentsKappa-conotoxin RIIIK
KeywordsTOXIN / cappa-conotoxin / protein
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Kappa-conotoxin RIIIK
Function and homology information
Biological speciesConus radiatus (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLushpa, V.A. / Vassilevski, A.A. / Bocharov, E.V. / Olivera, B.M. / Rivier, J. / Raghuraman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Solution structure of kappa-conotoxin RIIIK
Authors: Lushpa, V.A. / Vassilevski, A.A. / Bocharov, E.V. / Olivera, B.M. / Rivier, J. / Raghuraman, S.
History
DepositionNov 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kappa-conotoxin RIIIK


Theoretical massNumber of molelcules
Total (without water)2,6571
Polymers2,6571
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)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Kappa-conotoxin RIIIK / Kappa-M-RIIIK / Conotoxin R3.1


Mass: 2657.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus radiatus (invertebrata) / References: UniProt: P69769
Has ligand of interestY
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-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC aliphatic
142isotropic12D 1H-1H NOESY
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-13C HSQC aliphatic
172isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution195 % H2O, 5 % D-99.8% D2O, 0.001 % sodium azide, 95% H2O/5% D2Onatural abundance95% H2O/5% D2O
solution2100 % D-99.8% D2O, 0.001 % sodium azide, 100% D2Onatural abundance100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
95 %H2Onatural abundance1
5 %D2OD-99.8%1
0.001 %sodium azidenatural abundance1
100 %D2OD-99.8%2
0.001 %sodium azidenatural abundance2
Sample conditionsIonic strength: Null Not defined / Label: 1 / pH: 3.95 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
TopSpin3.4Bruker Biospincollection
CARA1.9.1.7Keller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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