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- PDB-1j5j: Solution structure of HERG-specific scorpion toxin BeKm-1 -

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Basic information

Entry
Database: PDB / ID: 1j5j
TitleSolution structure of HERG-specific scorpion toxin BeKm-1
ComponentsBeKm-1 toxin
KeywordsTOXIN / ALPHA-BETA MOTIF / CYSTEINE-KNOT MOTIF
Function / homologyScorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region / Potassium channel toxin gamma-KTx 2.1
Function and homology information
Biological speciesMesobuthus eupeus (lesser Asian scorpion)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsKorolokova, Y.V. / Bocharov, E.V. / Angelo, K. / Maslennikov, I.V. / Grinenko, O.V. / Lipkin, A.V. / Nosireva, E.D. / Pluzhnikov, K.A. / Olesen, S.-P. / Arseniev, A.S. / Grishin, E.V.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: New binding site on common molecular scaffold provides HERG channel specificity of scorpion toxin BeKm-1.
Authors: Korolkova, Y.V. / Bocharov, E.V. / Angelo, K. / Maslennikov, I.V. / Grinenko, O.V. / Lipkin, A.V. / Nosyreva, E.D. / Pluzhnikov, K.A. / Olesen, S.P. / Arseniev, A.S. / Grishin, E.V.
History
DepositionApr 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BeKm-1 toxin


Theoretical massNumber of molelcules
Total (without water)4,1041
Polymers4,1041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide BeKm-1 toxin


Mass: 4103.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus eupeus (lesser Asian scorpion)
Plasmid: PEZZ18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q9BKB7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
142DQF-COSY
1522D TOCSY
1622D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM BeKm-1, 90% H2O, 10% D2O90% H2O/10% D2O
21 mM BeKm-1, 99.9% D2O99.9% D2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3bVARIANcollection
VNMR5.3bVARIANprocessing
XEASY1.2.11Bartelsdata analysis
DYANA1.5Guentertstructure solution
FANTOM4Schaumannrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 653 restraints: 326/67 are NOE-derived upper/lower distance constraints, 68/46 backbone/sidechain dihedral angle restraints, 64/64 upper/lower distance ...Details: The structures are based on a total of 653 restraints: 326/67 are NOE-derived upper/lower distance constraints, 68/46 backbone/sidechain dihedral angle restraints, 64/64 upper/lower distance restraints from 23 (18 bb-bb, 5 bb-sc) hydrogen bonds, 9/9 upper/lower distance restraints from 3 SS-bonds.
NMR ensembleConformers submitted total number: 1

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