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- PDB-6urp: RDC refined solution structure of the insecticidal toxin Ta1a -

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Basic information

Entry
Database: PDB / ID: 6urp
TitleRDC refined solution structure of the insecticidal toxin Ta1a
ComponentsU1-agatoxin-Ta1a
KeywordsTOXIN / Disulfide-rich peptides / peptides / Residual dipolar couplings / RDCs
Function / homologyCrustacean CHH/MIH/GIH neurohormone - #20 / Crustacean CHH/MIH/GIH neurohormone / toxin activity / Orthogonal Bundle / extracellular region / Mainly Alpha / U1-agatoxin-Ta1a
Function and homology information
Biological speciesEratigena agrestis (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsRamanujam, V. / Shen, Y. / Ying, J. / Mobli, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Front Chem / Year: 2019
Title: Residual Dipolar Couplings for Resolving Cysteine Bridges in Disulfide-Rich Peptides.
Authors: Ramanujam, V. / Shen, Y. / Ying, J. / Mobli, M.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 23, 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

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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
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1medoid

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Components

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


Mass: 5781.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eratigena agrestis (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: O46166
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
111isotropic13D CT-HNCA
121isotropic22D IPAP-HSQC
231anisotropic12D IPAP-HSQC
341anisotropic12D IPAP-HSQC
151isotropic13D HNCO
261anisotropic13D HNCO
371anisotropic13D HNCO
181isotropic13D CT-HN(CO)CA
291anisotropic13D CT-HN(CO)CA
3101anisotropic13D CT-HN(CO)CA
1111isotropic12D 1H-15N TROSY
2121anisotropic12D 1H-15N TROSY
3131anisotropic12D 1H-15N TROSY
1141isotropic33D CT-HN(COCA)CB
2151anisotropic13D CT-HN(COCA)CB
1161isotropic33D HA[HB,HN](CACO)NH
1172isotropic23D HNHB

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM 13C/15N U1-agatoxin-Ta1a, 95% H2O/5% D2O13C/15N_sample95% H2O/5% D2O
solution20.5 mM 15N U1-agatoxin-Ta1a, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMU1-agatoxin-Ta1a13C/15N1
0.5 mMU1-agatoxin-Ta1a15N2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM phosphate buffer0 mMconditions_16.21 bar298 K
25.8 mg/ml of Pf1 phage, 20 mM phosphate buffer0 mMconditions_26.21 bar298 K
38% w/v of polyethylene glycol (PEG) based liquid crystal, 20 mM phosphate buffer0 mMconditions_36.21 bar298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCE IIIBrukerAVANCE III7003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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