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- PDB-1dl0: SOLUTION STRUCTURE OF THE INSECTICIDAL NEUROTOXIN J-ATRACOTOXIN-HV1C -

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Basic information

Entry
Database: PDB / ID: 1dl0
TitleSOLUTION STRUCTURE OF THE INSECTICIDAL NEUROTOXIN J-ATRACOTOXIN-HV1C
ComponentsJ-ATRACOTOXIN-HV1C
KeywordsTOXIN / NEUROTOXIN / ATRACOTOXIN / INSECTICIDAL / CYSTINE KNOT / VICINAL DISULFIDE
Function / homologyJanus-atracotoxin / Janus-atracotoxin / Janus-faced atracotoxin (J-ACTX) family signature. / potassium channel regulator activity / toxin activity / extracellular region / Lambda-hexatoxin-Hv1c
Function and homology information
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING
AuthorsWang, X.H. / King, G.F.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Discovery and characterization of a family of insecticidal neurotoxins with a rare vicinal disulfide bridge.
Authors: Wang, X. / Connor, M. / Smith, R. / Maciejewski, M.W. / Howden, M.E. / Nicholson, G.M. / Christie, M.J. / King, G.F.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: The Structure of a Novel Insecticidal Neurotoxin, Omega-Atracotoxin-HV1, from the Venom of an Australian Funnel Web Spider
Authors: Fletcher, J.I. / Smith, R. / O'Donoghue, S.I. / Nilges, M. / Connor, M. / Howden, M.E.H. / Christie, M.J. / King, G.F.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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
Revision 1.4Nov 6, 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: J-ATRACOTOXIN-HV1C


Theoretical massNumber of molelcules
Total (without water)3,7721
Polymers3,7721
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 J-ATRACOTOXIN-HV1C


Mass: 3772.317 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN THE SPIDER, HADRONYCHE VERSUTA. THE PEPTIDE WAS CHEMICALLY SYNTHESIZED FOR NMR STUDIES USING STANDARD T-BOC CHEMISTRY AND OXIDIZED/FOLDED IN A GLUTATHIONE REDOX BUFFER.
References: UniProt: P82228
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111H2O 2D NOESY
1212D TOCSY
131E-COSY
142D2O 2D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
11.6 MM J-ATRACOTOXIN-HV1C
21.6 MM J-ATRACOTOXIN-HV1C
Sample conditionsIonic strength: 0.005 / pH: 4.95 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2BRUKER ANALYTIK GMBHcollection
XwinNMR2BRUKER ANALYTIK GMBHprocessing
XEASY1.3.13XIA, BARTELSdata analysis
DYANA1.5GUENTERTstructure solution
X-PLOR3.8BRUNGERrefinement
MOLMOL2.6KORADIdata analysis
RefinementMethod: DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 403 NOE-DERIVED DISTANCE RESTRAINTS, 41 DIHEDRAL-ANGLE RESTRAINTS, PLUS 56 RESTRAINTS DEFINING 14 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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