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- PDB-5we3: Solution NMR structure of PaurTx-3 -

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Basic information

Entry
Database: PDB / ID: 5we3
TitleSolution NMR structure of PaurTx-3
ComponentsBeta-theraphotoxin-Ps1a
KeywordsTOXIN / Disulfide rich peptides / pain / rational drug design / serum stability / spider venom / voltage-gated ion channels / trimolecular complex
Function / homologyHuwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin / sodium channel inhibitor activity / : / toxin activity / extracellular space / Beta-theraphotoxin-Ps1a
Function and homology information
Biological speciesParaphysa scrofa (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsAgwa, A.J. / Schroeder, C.I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1080405 Australia
CitationJournal: Toxins (Basel) / Year: 2017
Title: Lengths of the C-Terminus and Interconnecting Loops Impact Stability of Spider-Derived Gating Modifier Toxins.
Authors: Agwa, A.J. / Huang, Y.H. / Craik, D.J. / Henriques, S.T. / Schroeder, C.I.
History
DepositionJul 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-theraphotoxin-Ps1a


Theoretical massNumber of molelcules
Total (without water)4,0731
Polymers4,0731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Beta-theraphotoxin-Ps1a / Beta-TRTX-Ps1a / Phrixotoxin-3 / PaurTx3


Mass: 4072.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Paraphysa scrofa (spider) / References: UniProt: P84510

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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 NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H NOESY
172isotropic12D 1H-13C HSQC
182isotropic11D 1H
1141isotropic12D ECOSY
291isotropic12D 1H-1H TOCSY
3101isotropic12D 1H-1H TOCSY
4111isotropic12D 1H-1H TOCSY
5121isotropic12D 1H-1H TOCSY
6131isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mg/mL PaurTx-3, 90% H2O/10% D2OPaurTx-390% H2O/10% D2O
solution21 mg/mL PaurTx-3, 100% D2OPaurTx-3 _D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mLPaurTx-3natural abundance1
1 mg/mLPaurTx-3natural abundance2
Sample conditions
Conditions-IDIonic strength unitsLabelpHPressure (kPa)Temperature (K)
1Not definedconditions_14 ambient mmHg298 K
6Not definedconditions_64 ambient mmHg308 K
5Not definedconditions_54 ambient mmHg303 K
4Not definedconditions_44 ambient mmHg293 K
3Not definedconditions_34 ambient mmHg288 K
2Not definedconditions_24 ambient mmHg283 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
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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