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- PDB-1v4q: Three-dimensional solution structure of the analogue peptide of o... -

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Basic information

Entry
Database: PDB / ID: 1v4q
TitleThree-dimensional solution structure of the analogue peptide of omega-conotoxin MVIIC
Componentsomega-conotoxin MVIIC
KeywordsTOXIN / omega-conotoxin / cystine knot motif / triple-stranded antiparallel beta-sheet / calcium channel blocker
Function / homologyConotoxin, omega-type, conserved site / Omega-conotoxin family signature. / host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region / Omega-conotoxin MVIIC
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKobayashi, K. / Sasaki, T. / Sato, K. / Kohno, T.
CitationJournal: To be Published
Title: Three-dimensional solution structure of the analogue peptide of omega-conotoxin MVIIC
Authors: Kobayashi, K. / Sasaki, T. / Sato, K. / Kohno, T.
History
DepositionNov 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: omega-conotoxin MVIIC


Theoretical massNumber of molelcules
Total (without water)2,9021
Polymers2,9021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide omega-conotoxin MVIIC


Mass: 2901.580 Da / Num. of mol.: 1 / Mutation: S17K/S19R/K25R / Source method: obtained synthetically / Details: This peptide was chemically synthesized. / References: UniProt: P37300
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
1422D NOESY
152DQF-COSY
1622D TOCSY
172PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
19mM omega-conotoxin MVIIC analogue; 90% H2O, 10% D2O90% H2O/10% D2O
29mM omega-conotoxin MVIIC analogue; D2OD2O
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 288 K

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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
NMRPipe2002Delaglioprocessing
PIPP4.3.2Garrettdata analysis
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 562 restraints, 536 are NOE-derived distance constraints, 18 dihedral angle restraints, 8 distance restraints from hydrogen bonds and disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 18

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