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- PDB-2km9: Omega conotoxin-FVIA -

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Basic information

Entry
Database: PDB / ID: 2km9
TitleOmega conotoxin-FVIA
Componentsomega_conotoxin-FVIA
KeywordsNEUROPEPTIDE / omega conotoxin / FVIA
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLee, S. / Kim, J. / Lee, J. / Jung, H.
CitationJournal: To be Published
Title: Structure of omega conotoxin-FVIA
Authors: Lee, S. / Lee, J. / Jung, H. / Kim, J.
History
DepositionJul 25, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Structure summary
Revision 1.3Nov 6, 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: omega_conotoxin-FVIA


Theoretical massNumber of molelcules
Total (without water)2,5791
Polymers2,5791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide omega_conotoxin-FVIA


Mass: 2579.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
141PE-COSY

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Sample preparation

DetailsContents: 7mM omega conotoxin-FVIA-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 7 mM / Component: omega conotoxin-FVIA-1
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 298 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 softwareName: X-PLOR / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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