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- PDB-1koz: SOLUTION STRUCTURE OF OMEGA-GRAMMOTOXIN SIA -

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Entry
Database: PDB / ID: 1koz
TitleSOLUTION STRUCTURE OF OMEGA-GRAMMOTOXIN SIA
ComponentsVoltage-dependent Channel Inhibitor
KeywordsTOXIN / CYSTINE KNOT
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / potassium channel inhibitor activity / sodium channel regulator activity / calcium channel inhibitor activity / toxin activity / extracellular region / Omega-theraphotoxin-Gr1a
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsTakeuchi, K. / Park, E.J. / Lee, C.W. / Kim, J.I. / Takahashi, H. / Swartz, K.J. / Shimada, I.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Solution structure of omega-grammotoxin SIA, a gating modifier of P/Q and N-type Ca(2+) channel.
Authors: Takeuchi, K. / Park, E. / Lee, C. / Kim, J. / Takahashi, H. / Swartz, K. / Shimada, I.
History
DepositionDec 25, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 16, 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:
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Assembly

Deposited unit
A: Voltage-dependent Channel Inhibitor


Theoretical massNumber of molelcules
Total (without water)4,1231
Polymers4,1231
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 Voltage-dependent Channel Inhibitor / omega-Grammotoxin SIA


Mass: 4122.778 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized by a solid-phase methodology
References: UniProt: P60590
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
121E-COSY
1312D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 2.4mM Grammotoxin NA; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: 1 atm / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
ANSIG3.3Kraulisdata analysis
XwinNMR1.3Brukercollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 561 restraints, 536 are NOE-derived distance constraints, 20 dihedral angle ...Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 561 restraints, 536 are NOE-derived distance constraints, 20 dihedral angle restraints,5 distance restraints from hydrogen bonds.
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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