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- PDB-1g92: SOLUTION STRUCTURE OF PONERATOXIN -

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Basic information

Entry
Database: PDB / ID: 1g92
TitleSOLUTION STRUCTURE OF PONERATOXIN
ComponentsPONERATOXIN
KeywordsTOXIN / Neurotoxin / Sodium channel inhibitor
Function / homologyhost cell postsynaptic membrane / host cell presynaptic membrane / sodium channel regulator activity / toxin activity / extracellular region / Glycyl-poneratoxin
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsSzolajska, E. / Poznanski, J. / Ferber, M.L. / Michalik, J. / Gout, E. / Fender, P. / Bailly, I. / Dublet, B. / Chroboczek, J.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Poneratoxin, a neurotoxin from ant venom. Structure and expression in insect cells and construction of a bio-insecticide.
Authors: Szolajska, E. / Poznanski, J. / Ferber, M.L. / Michalik, J. / Gout, E. / Fender, P. / Bailly, I. / Dublet, B. / Chroboczek, J.
History
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PONERATOXIN


Theoretical massNumber of molelcules
Total (without water)2,7591
Polymers2,7591
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)10 / 333target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PONERATOXIN / PAC-TX


Mass: 2759.355 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Paraponera clavata (Venon ant).
References: UniProt: P41736

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. 100 and 200 ms mixing time 2D-NOESY spectra were accumulated

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Sample preparation

DetailsContents: 3 mM of C-amidated peptide / Solvent system: D2O:TFE in volumetric ratio 3:1
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 298 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 AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR930601.3Brukercollection
NMRPipe1.7Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
XEASY1.3.11Bartels, Xia, Guntert, Billeter, Wuthrichdata analysis
DYANA1.5Guntert, Mumenthalerstructure solution
X-PLOR3.1Brungerrefinement
SYBYL6.5Biosymdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 428 NOE-derived distance restraints and 20 dihedral angle restraints. Simulated annealing in the REDAC strategy made by DYANA. Final refinement, inculding PRO ...Details: The structures are based on 428 NOE-derived distance restraints and 20 dihedral angle restraints. Simulated annealing in the REDAC strategy made by DYANA. Final refinement, inculding PRO pyrrolidine ring puckering by X-PLOR.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 333 / Conformers submitted total number: 10

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