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- PDB-2mld: Solution structure of BmKTX-D19K/K6D -

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Basic information

Entry
Database: PDB / ID: 2mld
TitleSolution structure of BmKTX-D19K/K6D
ComponentsPotassium channel toxin alpha-KTx 3.6
KeywordsTOXIN
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / potassium channel inhibitor activity / Knottin, scorpion toxin-like superfamily / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 3.6
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsHong, J. / Lin, D. / Chen, Z. / Wu, Y.
CitationJournal: To be Published
Title: SOLUTION STRUCTURE of BMKTX-D19K
Authors: Hong, J. / Lin, D. / Chen, Z. / Wu, Y.
History
DepositionFeb 24, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 3.6


Theoretical massNumber of molelcules
Total (without water)3,9781
Polymers3,9781
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 3.6 / BmKTX / Kaliotoxin


Mass: 3977.834 Da / Num. of mol.: 1 / Fragment: UNP residues 23-59 / Mutation: K6D, D19K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9NII7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 2 mM entity-1, 10 % [U-99% 2H] D2O-2, 90 % H2O-3, 25 mM potassium phosphate-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMentity-11
10 %D2O-2[U-99% 2H]1
90 %H2O-31
25 mMpotassium phosphate-41
Sample conditionsIonic strength: 0.025 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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