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- PDB-1g9p: SOLUTION STRUCTURE OF THE INSECTICIDAL CALCIUM CHANNEL BLOCKER OM... -

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Basic information

Entry
Database: PDB / ID: 1g9p
TitleSOLUTION STRUCTURE OF THE INSECTICIDAL CALCIUM CHANNEL BLOCKER OMEGA-ATRACOTOXIN-HV2A
ComponentsOMEGA-ATRACOTOXIN-HV2A
KeywordsTOXIN / cystine knot
Function / homology
Function and homology information


sodium channel inhibitor activity / calcium channel inhibitor activity / toxin activity / extracellular region
Similarity search - Function
Omega-atracotoxin, conserved site-2 / Omega-atracotoxin (ACTX) type 2 family signature. / Magi 5 toxic peptide / Magi 5 toxic peptide family / Omega-AgatoxinV - #10 / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Omega-hexatoxin-Hv2a
Similarity search - Component
Biological speciesHadronyche versuta (spider)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, DYNAMICAL SIMULATED ANNEALING
AuthorsWang, X.-H. / King, G.F.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Discovery and structure of a potent and highly specific blocker of insect calcium channels.
Authors: Wang, X.H. / Connor, M. / Wilson, D. / Wilson, H.I. / Nicholson, G.M. / Smith, R. / Shaw, D. / Mackay, J.P. / Alewood, P.F. / Christie, M.J. / King, G.F.
History
DepositionNov 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OMEGA-ATRACOTOXIN-HV2A


Theoretical massNumber of molelcules
Total (without water)4,4881
Polymers4,4881
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 OMEGA-ATRACOTOXIN-HV2A


Mass: 4488.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hadronyche versuta (spider) / References: UniProt: P82852

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111H2O 2D NOESY
121D2O 2D NOESY
2312D TOCSY
241E-COSY
152DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear NMR techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM omega-atracotoxin-Hv2a95% H2O, 5% D2O, 5 micromolar chloramphenicol, 100 micromolar TSP
21.2 mM omega-atracotoxin-Hv2a100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.005 4.71 1 atm296 K
20.005 4.71 1 atm288 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Bruker Analytik GmbHcollection
XwinNMR2Bruker Analytik GmbHprocessing
Felix97Molecular Simulations Inc.processing
XEASY1.3.13Tai-he Xia & Christian Bartelsdata analysis
DYANA1.5Peter Guentertstructure solution
X-PLOR3.1Axel Brungerrefinement
VNMR6.1BVarian Inc.collection
RefinementMethod: TORSION ANGLE DYNAMICS, DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
Details: The structures are based on a total of 430 NOE-derived distance restraints, 34 dihedral-angle restraints, plus 24 restraints defining 12 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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