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- PDB-1g1z: NMR Solution Structures of delta-Conotoxin EVIA from Conus ermine... -

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Basic information

Entry
Database: PDB / ID: 1g1z
TitleNMR Solution Structures of delta-Conotoxin EVIA from Conus ermineus that Selectively Acts on Vertebrate Neuronal Na+ Channels, LEU12-PRO13 Cis isomer
ComponentsCONOTOXIN EVIA
KeywordsTOXIN / three disulfide linkages / cis/trans isomerism of Leu12-Pro13 peptide bond / hydroxyproline
Function / homologyConotoxin, delta-type, conserved site / Delta-conotoxin family signature. / sodium channel inhibitor activity / toxin activity / extracellular region / Delta-conotoxin EVIA
Function and homology information
MethodSOLUTION NMR / hybrid distance geometry dynamical simulated annealing with the allhdg force field, simulated annealing with the CHARMM22 force field
AuthorsVolpon, L. / Lamthanh, H. / Le Gall, F. / Menez, A. / Lancelin, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: NMR Solution Structures of delta-Conotoxin EVIA from Conus ermineus That Selectively Acts on Vertebrate Neuronal Na+ Channels.
Authors: Volpon, L. / Lamthanh, H. / Barbier, J. / Gilles, N. / Lancelin, J.M.
#1: Journal: To be Published
Title: Conotoxin EVIA, a Novel Peptide from Conus ermineus Venom that Preferentially Acts on Neuronal Voltage-dependent Sodium Channels
Authors: Barbier, J. / Lamthanh, H. / Le Gall, F. / Favreau, P. / Benoit, E. / Chen, H. / Gilles, N. / Ilan, N. / Heinemann, S.F. / Gordon, D. / Menez, A. / Molgo, J.
History
DepositionOct 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CONOTOXIN EVIA


Theoretical massNumber of molelcules
Total (without water)3,2951
Polymers3,2951
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)18 / 30structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #14closest to the average

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Components

#1: Protein/peptide CONOTOXIN EVIA


Mass: 3294.909 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The solid phase synthesis of conotoxin EVIA was carried out using the F-moc chemistry. The sequence of the peptide is naturally found in Conus ermineus (Atlantic fish-hunting cone).
References: UniProt: P60513

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2 mM conotoxin EVIA; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.01 / pH: 3 / Pressure: ambient / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Gifa4.22Delsucdata analysis
X-PLOR3.851Brungerrefinement
CHARMM22Brooksrefinement
RefinementMethod: hybrid distance geometry dynamical simulated annealing with the allhdg force field, simulated annealing with the CHARMM22 force field
Software ordinal: 1
Details: the structures are based on a total of 257 restraints, 211 are NOE-derived distance constraints, 24 dihedral angle restraints, 22 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 18

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