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- PDB-2kir: Solution structure of a designer toxin, mokatoxin-1 -

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Basic information

Entry
Database: PDB / ID: 2kir
TitleSolution structure of a designer toxin, mokatoxin-1
ComponentsDesigner toxin
KeywordsTOXIN / venom / scorpion / phage display / mokatoxin / moka1
Biological speciessynthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBiancalana, M. / Koide, A. / Takacs, Z. / Goldstein, S. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library.
Authors: Takacs, Z. / Toups, M. / Kollewe, A. / Johnson, E. / Cuello, L.G. / Driessens, G. / Biancalana, M. / Koide, A. / Ponte, C.G. / Perozo, E. / Gajewski, T.F. / Suarez-Kurtz, G. / Koide, S. / Goldstein, S.A.
History
DepositionMay 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3Oct 9, 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: Designer toxin


Theoretical massNumber of molelcules
Total (without water)3,8911
Polymers3,8911
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Designer toxin


Mass: 3890.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.3 mM [U-13C; U-15N] Moka1-1, 10 mM sodium phosphate-2, 7 % D2O-3, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMMoka1-1[U-13C; U-15N]1
10 mMsodium phosphate-21
7 %D2O-31
Sample conditionsIonic strength: 15 / pH: 6 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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