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- PDB-6efe: NMR Solution Structure of vil14a -

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Basic information

Entry
Database: PDB / ID: 6efe
TitleNMR Solution Structure of vil14a
ComponentsKappa-conotoxin vil14a
KeywordsTOXIN / vil14a / Cone snails / F14 conotoxins / R-superfamily / nanoNMR / structural convergence
Function / homologytoxin activity / extracellular region / Conotoxin vil14a
Function and homology information
Biological speciesConus villepinii (invertebrata)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDovell, S. / Mari, F. / Moller, C. / Melaun, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM 066004 United States
Other governmentR/LR-MB-28 United States
CitationJournal: Peptides / Year: 2018
Title: Definition of the R-superfamily of conotoxins: Structural convergence of helix-loop-helix peptidic scaffolds.
Authors: Moller, C. / Dovell, S. / Melaun, C. / Mari, F.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 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: Kappa-conotoxin vil14a


Theoretical massNumber of molelcules
Total (without water)2,8791
Polymers2,8791
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)18 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Kappa-conotoxin vil14a


Mass: 2879.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus villepinii (invertebrata) / References: UniProt: P84704

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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 NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 1 mM NA peptide, 0.11 mM TSP, 90% H2O/10% D2O / Label: 1H_vil14a / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpeptideNA1
0.11 mMTSPnatural abundance1
Sample conditionsIonic strength: water solution Not defined / Label: conditions_1 / pH: 3.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
VNMRVarianprocessing
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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