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- PDB-2ksl: Structure of the insecticidal toxin TaITX-1 -

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Basic information

Entry
Database: PDB / ID: 2ksl
TitleStructure of the insecticidal toxin TaITX-1
ComponentsU1-agatoxin-Ta1a
KeywordsTOXIN / insecticidal toxin / spider toxin / neurotoxin / crustacean hyperglycemic hormone / molt-inhibiting hormone / Disulfide bond / Secreted
Function / homologyCrustacean CHH/MIH/GIH neurohormone - #20 / Crustacean CHH/MIH/GIH neurohormone / toxin activity / extracellular region / Orthogonal Bundle / Mainly Alpha / U1-agatoxin-Ta1a
Function and homology information
Biological speciesTegenaria agrestis (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsBEST MOLPROBITY SCORE, model 1
AuthorsMobli, M. / King, G.F.
CitationJournal: Structure / Year: 2015
Title: Weaponization of a Hormone: Convergent Recruitment of Hyperglycemic Hormone into the Venom of Arthropod Predators
Authors: Undheim, E.A. / Grimm, L.L. / Low, C.F. / Morgenstern, D. / Herzig, V. / Zobel-Thropp, P. / Pineda, S.S. / Habib, R. / Dziemborowicz, S. / Fry, B.G. / Nicholson, G.M. / Binford, G.J. / Mobli, M. / King, G.F.
History
DepositionJan 7, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 3, 2012Group: Structure summary
Revision 1.3Jun 24, 2015Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U1-agatoxin-Ta1a


Theoretical massNumber of molelcules
Total (without water)5,7811
Polymers5,7811
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)25 / 200BEST MOLPROBITY SCORE
RepresentativeModel #1best molprobity score

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Components

#1: Protein U1-agatoxin-Ta1a / U1-AGTX-Ta1a / Paralytic insecticidal toxin 1 / TaITX-1


Mass: 5781.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tegenaria agrestis (spider)
Description: The toxin was produced by overexpression in the periplasm of Escherichia coli.
Gene: ITX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O46166
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the insecticidal neurotoxin TaITX-1 determined using heteronuclear NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCO
1413D 1H-15N NOESY
1514D HCC(CO)NH
1612D 1H-15N HSQC
1723D 1H-13C NOESY
NMR detailsText: Mixing times were 200 ms (3D NOESY) and 12 ms (4D HCC(CO)NH).

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Sample preparation

Details
Solution-IDContentsSolvent system
1150 uM [U-100% 13C; U-100% 15N] Ta1a-1, 95% H2O/5% D2O95% H2O/5% D2O
2150 uM [U-100% 13C; U-100% 15N] Ta1a-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMTa1a-1[U-100% 13C; U-100% 15N]1
150 uMTa1a-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 1 / pH: 4.4 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1P.GUNTERT ET AL.noesy assignment
CYANA2.1P.GUNTERT ET AL.structure solution
CYANA2.1P.GUNTERT ET AL.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 574 / NOE intraresidue total count: 183 / NOE long range total count: 88 / NOE medium range total count: 137 / NOE sequential total count: 166 / Disulfide bond constraints total count: 9 / Hydrogen bond constraints total count: 36 / Protein chi angle constraints total count: 20 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: best molprobity score
NMR ensembleConformer selection criteria: BEST MOLPROBITY SCORE / Conformers calculated total number: 200 / Conformers submitted total number: 25 / Representative conformer: 1

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