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- PDB-6px8: Dg3b in Weaponisation 'on the fly': Convergent recruitment of kno... -

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Basic information

Entry
Database: PDB / ID: 6px8
TitleDg3b in Weaponisation 'on the fly': Convergent recruitment of knottin and defensin scaffolds as neurotoxins in the venom of assassin fly Dolopus genitalis (Diptera: Asilidae)
ComponentsVenom polypeptide
KeywordsTOXIN / disulfide-rich / assassin-fly / defensin / ultra-stable peptide
Function / homology
Function and homology information


humoral immune response / potassium channel regulator activity / toxin activity / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
Biological speciesDolopus genitalis (fry)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAgwa, A.J. / Schroeder, C.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2019
Title: Weaponisation 'on the fly': Convergent recruitment of knottin and defensin peptide scaffolds into the venom of predatory assassin flies.
Authors: Jin, J. / Agwa, A.J. / Szanto, T.G. / Csoti, A. / Panyi, G. / Schroeder, C.I. / Walker, A.A. / King, G.F.
History
DepositionJul 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Venom polypeptide


Theoretical massNumber of molelcules
Total (without water)4,1481
Polymers4,1481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Venom polypeptide


Mass: 4147.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dolopus genitalis (fry) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G5BIB1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HSQC
151isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1 mg/mL 0 Dg3b, 90% H2O/10% D2O / Label: Dg3b / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mg/mL / Component: Dg3b / Isotopic labeling: 0
Sample conditionsIonic strength: 0 M / Label: Dg3b / pH: 4 / Pressure: 1 Pa / Temperature: 298 K

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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
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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