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- PDB-2lix: Solution structure Analysis of the ImKTx104 -

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Basic information

Entry
Database: PDB / ID: 2lix
TitleSolution structure Analysis of the ImKTx104
ComponentsPotassium Channel Toxins
KeywordsTOXIN / disulfide bond stabilized structure
Function / homologypotassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 28.1
Function and homology information
Biological speciesLychas mucronatus (Chinese swimming scorpion)
MethodSOLUTION NMR / simulated annealing, energy minimization
Model detailsclosest to the mean of the 20 conformers, model 8
AuthorsZeng, D.Y. / Jiang, L.
CitationJournal: Plos One / Year: 2012
Title: Structural and functional diversity of acidic scorpion potassium channel toxins.
Authors: Chen, Z.Y. / Zeng, D.Y. / Hu, Y.T. / He, Y.W. / Pan, N. / Ding, J.P. / Cao, Z.J. / Liu, M.L. / Li, W.X. / Yi, H. / Jiang, L. / Wu, Y.L.
History
DepositionSep 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium Channel Toxins


Theoretical massNumber of molelcules
Total (without water)2,9291
Polymers2,9291
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 / 20020 structures for lowest energy
RepresentativeModel #1closest to the mean of the 20 conformers

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Components

#1: Protein/peptide Potassium Channel Toxins / ImKTx104


Mass: 2929.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lychas mucronatus (Chinese swimming scorpion)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: R4GUQ3*PLUS
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited 3D NOESY-HSQC
12115N,1H-HSQC
1311H,1H-TOCSY
1411H,1H-NOESY

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Sample preparation

DetailsContents: 2 mM [U-15N] entity_1-1, 20 mM sodium phosphate-2, 90% v/v H2O-3, 10% v/v [U-99% 2H] D2O-4, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity_1-1[U-15N]1
20 mMsodium phosphate-21
90 v/vH2O-31
10 v/vD2O-4[U-99% 2H]1
Sample conditionspH: 5 / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert, P. / Classification: refinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: 200 structures were calculated with the Cyana 2.1 program starting from randomly generated conformers in 10,000 annealing steps, 20 conformoers with minimal target functions were selected to ...Details: 200 structures were calculated with the Cyana 2.1 program starting from randomly generated conformers in 10,000 annealing steps, 20 conformoers with minimal target functions were selected to undergo energy minimization using the AMBER force field
NMR representativeSelection criteria: closest to the mean of the 20 conformers
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 8

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