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- PDB-1rji: Solution Structure of BmKX, a novel potassium channel blocker fro... -

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Basic information

Entry
Database: PDB / ID: 1rji
TitleSolution Structure of BmKX, a novel potassium channel blocker from the Chinese Scorpion Buthus martensi Karsch
Componentspotassium channel toxin KX
KeywordsTOXIN / 3-10 helix / beta sheet
Function / homologyKnottin, scorpion toxin-like superfamily / extracellular region / Neurotoxin BmP08
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
Model type detailsminimized average
AuthorsCai, Z. / Wu, J. / Xu, Y. / Wang, C.-G. / Chi, C.-W. / Shi, Y.
CitationJournal: Toxicon / Year: 2005
Title: A novel short-chain peptide BmKX from the Chinese scorpion Buthus martensi karsch, sequencing, gene cloning and structure determination
Authors: Wang, C.-G. / Cai, Z. / Lu, W. / Wu, J. / Xu, Y. / Shi, Y. / Chi, C.-W.
History
DepositionNov 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: potassium channel toxin KX


Theoretical massNumber of molelcules
Total (without water)3,3341
Polymers3,3341
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)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide potassium channel toxin KX / BmKX


Mass: 3333.882 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in the Chinese Scorpion Buthus martensi Karsch
References: UniProt: Q7Z0H4
Has protein modificationY

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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
2422D TOCSY
252E-COSY
2622D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
1Phosphate buffer pH 5.0; 3mM BmKX90% H2O/10% D2O
2Phosphate buffer pH 5.0; 3mM BmKX99.96% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM phosphate 51 atm300 K
250mM phosphate 51 atm300 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: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASY3.2K. Wuthrichdata analysis
DIANA2.8K. Wuthrichdata analysis
CNS1Brunger, A.T.structure solution
CNS1Brunger, A.T.refinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: the structures are based on a total of 283 restraints, 245 are NOE-derived distance constraints, 19 dihedral angle restraints,19 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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