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- PDB-2li3: Structural and functional analysis of a novel potassium toxin arg... -

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Basic information

Entry
Database: PDB / ID: 2li3
TitleStructural and functional analysis of a novel potassium toxin argentinean scorpion Tityus trivittatus reveals a new kappa sub-family
ComponentsPotassium channel toxin kappa-KTX3.1
KeywordsTOXIN / ALPHA/ALPHA MOTIF / ALPHA SCORPION TOXIN / VOLTAGE GATED POTASSIUM CHANNEL ALPHA TOXIN
Function / homologytoxin activity / extracellular region / Kappa-buthitoxin-Tt2b
Function and homology information
Biological speciesTityus trivittatus (scorpion)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS
Model detailslowest energy, model 1
AuthorsSaucedo-Yanez, A. / Del Rio-Portilla, F. / Hernandez-Lopez, R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: New Tricks of an Old Pattern: STRUCTURAL VERSATILITY OF SCORPION TOXINS WITH COMMON CYSTEINE SPACING.
Authors: Saucedo, A.L. / Flores-Solis, D. / Rodriguez de la Vega, R.C. / Ramirez-Cordero, B. / Hernandez-Lopez, R. / Cano-Sanchez, P. / Navarro, R.N. / Garcia-Valdes, J. / Coronas-Valderrama, F. / de ...Authors: Saucedo, A.L. / Flores-Solis, D. / Rodriguez de la Vega, R.C. / Ramirez-Cordero, B. / Hernandez-Lopez, R. / Cano-Sanchez, P. / Navarro, R.N. / Garcia-Valdes, J. / Coronas-Valderrama, F. / de Roodt, A. / Brieba, L.G. / Possani, L.D. / Del Rio-Portilla, F.
History
DepositionAug 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin kappa-KTX3.1


Theoretical massNumber of molelcules
Total (without water)3,3351
Polymers3,3351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST TARGET FUNCTION
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel toxin kappa-KTX3.1


Mass: 3334.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tityus trivittatus (scorpion) / Production host: Escherichia coli (E. coli) / References: UniProt: B3A0L5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-1H TOCSY
1312D DQF-C

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Sample preparation

DetailsContents: 2.3 mM KAPPA-KTX3.1 SCORPION TOXIN, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 2.3 mM / Component: KAPPA-KTX3.1 SCORPION TOXIN-1
Sample conditionspH: 3.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA5001
Varian UNITYVarianUNITY5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1D.A.CASE, ET AL.refinement
NMRPipeDelaglio, Zhengrong and Baxstructure solution
XEASYBartels et al.structure solution
CARA1.5Keller and Wuthrichstructure solution
AMBER9Guntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure solution
AMBERGuntert, Mumenthaler and Wuthrichrefinement
CYANA2.1D.A.CASE, ET AL.structure solution
RefinementMethod: TORSION ANGLE DYNAMICS, MOLECULAR DYNAMICS / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED USING CYANA 2.1.THE 20 STRUCTURES OF 200 WITH LOWEST TARGET FUNCTION WERE REFINED BY MOLECULAR DYNAMICS WITH EXPLICIT SOLVENT USING AMBER 9.0.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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