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- PDB-8uxr: TxVIIB,U-superfamily conotoxin -

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Basic information

Entry
Database: PDB / ID: 8uxr
TitleTxVIIB,U-superfamily conotoxin
ComponentsConotoxin Tx6.5
KeywordsTOXIN
Function / homologytoxin activity / extracellular region / Conotoxin Tx6.5
Function and homology information
Biological speciesConus textile (cloth-of-gold cone)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRaffaelli, T. / Daly, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural analysis of a U-superfamily conotoxin containing a mini-granulin fold: Insights into key features that distinguish between the ICK and granulin folds.
Authors: Raffaelli, T. / Wilson, D.T. / Dutertre, S. / Giribaldi, J. / Vetter, I. / Robinson, S.D. / Thapa, A. / Widi, A. / Loukas, A. / Daly, N.L.
History
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Database references / Category: citation / database_2 / Item: _citation.journal_volume / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conotoxin Tx6.5


Theoretical massNumber of molelcules
Total (without water)2,4961
Polymers2,4961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Conotoxin Tx6.5


Mass: 2495.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus textile (cloth-of-gold cone) / References: UniProt: P0DPM3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D COSY
121anisotropic12D TOCSY
131anisotropic12D NOESY
141anisotropic12D 1H-13C HSQC
151anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 0.2 mM TxVIIB, 90% H2O/10% D2O / Label: TxVIIB / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.2 mM / Component: TxVIIB / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: 90% H2O/10% D2O / pH: 4 / Pressure: AMBIENT / Temperature: 290 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
NameVersionDeveloperClassification
TopSpin3.98.15Bruker Biospincollection
CcpNmr Analysis3.98.15CCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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