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- PDB-5l34: Calculated solution structure of [D-Trp3]-Contryphan-Vc2 -

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Basic information

Entry
Database: PDB / ID: 5l34
TitleCalculated solution structure of [D-Trp3]-Contryphan-Vc2
Components[D-Trp3]-Contryphan-Vc2
KeywordsTOXIN / Conus peptide / peptide toxin
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / : / toxin activity / lipid binding / extracellular region / Contryphan-Vc2
Function and homology information
Biological speciesConus victoriae (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsDrane, S.B. / Chhabra, S. / MacRaild, C.A.
CitationJournal: Toxicon / Year: 2017
Title: Structure and activity of contryphan-Vc2: Importance of the d-amino acid residue.
Authors: Drane, S.B. / Robinson, S.D. / MacRaild, C.A. / Chhabra, S. / Chittoor, B. / Morales, R.A. / Leung, E.W. / Belgi, A. / Espino, S.S. / Olivera, B.M. / Robinson, A.J. / Chalmers, D.K. / Norton, R.S.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [D-Trp3]-Contryphan-Vc2


Theoretical massNumber of molelcules
Total (without water)8631
Polymers8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint1 kcal/mol
Surface area940 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide [D-Trp3]-Contryphan-Vc2


Mass: 863.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus victoriae (invertebrata) / References: UniProt: W4VSA0*PLUS

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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 ROESY
341isotropic12D 1H-15N SOFAST-HMQC
252isotropic12D 1H-13C HSQC
232isotropic12D DQF-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 M [D-Trp3]-Contryphan-Vc2, 93% H2O/7% D2OH2O_sample93% H2O/7% D2O
solution22.0 M [D-Trp3]-Contryphan-Vc2, 100% D2OD2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 M[D-Trp3]-Contryphan-Vc2natural abundance1
2.0 M[D-Trp3]-Contryphan-Vc2natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 M5C4.0 1 atm278 K
20 M10C-4.04.0 1 atm283 K
30 M10C-4.14.1 1 atm283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospincollection
Analysis2.1.5CCPNpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH2.4Schwieters, Kuszewski, Tjandra and Clorerefinement
Analysis2.1.5CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 4
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: 20

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