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- PDB-1ie6: SOLUTION STRUCTURE OF IMPERATOXIN A -

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Basic information

Entry
Database: PDB / ID: 1ie6
TitleSOLUTION STRUCTURE OF IMPERATOXIN A
ComponentsIMPERATOXIN A
KeywordsTOXIN / Triple stranded antiparellel beta-sheet / inhibitory cystine knot
Function / homologyScorpion calcine / Scorpion calcine family / Scorpion calcine family signature. / calcium channel inhibitor activity / toxin activity / extracellular region / Imperacalcin
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsLee, C.W. / Takeuchi, K. / Takahashi, H. / Sato, K. / Shimada, I. / Kim, D.H. / Kim, J.I.
CitationJournal: Biochem.J. / Year: 2004
Title: Molecular basis of the high-affinity activation of type 1 ryanodine receptors by imperatoxin A.
Authors: Lee, C.W. / Lee, E.H. / Takeuchi, K. / Takahashi, H. / Shimada, I. / Sato, K. / Shin, S.Y. / Kim, D.H. / Kim, J.I.
History
DepositionApr 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: 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 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
Remark 999SEQUENCE The sequence of this protein was published in a journal (Zamudio, F. Z., et al. 1997, FEBS ...SEQUENCE The sequence of this protein was published in a journal (Zamudio, F. Z., et al. 1997, FEBS Lett. 405, 385-389).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMPERATOXIN A


Theoretical massNumber of molelcules
Total (without water)3,7761
Polymers3,7761
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 / 100The submitted conformer models are those with the lowest energy and the least restraint violations.
RepresentativeModel #11closest to the average

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Components

#1: Protein/peptide IMPERATOXIN A / PEPTIDE NEUROTOXIN / RYANODINE RECEPTOR ACTIVATOR


Mass: 3776.495 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in the venom of scorpion Pandinus imperator.
References: UniProt: P59868
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5mM Imperatoxin A; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.4 / Pressure: ambient / Temperature: 300 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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
XwinNMR3Brukerprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 519 restraints, 473 are NOE-derived distance constraints, 25 dihedral angle restraints, 12 distance restraints from hydrogen bonds, and 9 distance ...Details: The structures are based on a total of 519 restraints, 473 are NOE-derived distance constraints, 25 dihedral angle restraints, 12 distance restraints from hydrogen bonds, and 9 distance restraints form disulfide bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are those with the lowest energy and the least restraint violations.
Conformers calculated total number: 100 / Conformers submitted total number: 20

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