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- PDB-1rmk: Solution structure of conotoxin MrVIB -

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Basic information

Entry
Database: PDB / ID: 1rmk
TitleSolution structure of conotoxin MrVIB
ComponentsMu-O-conotoxin MrVIB
KeywordsTOXIN / beta sheet / cystine knot
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region / Mu-conotoxin MrVIB
Function and homology information
Biological speciesConus marmoreus (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsDaly, N.L. / Ekberg, J.A. / Thomas, L. / Adams, D.J. / Lewis, R.J. / Craik, D.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structures of muO-conotoxins from Conus marmoreus. Inhibitors of tetrodotoxin (TTX)-sensitive and TTX-resistant sodium channels in mammalian sensory neurons
Authors: Daly, N.L. / Ekberg, J.A. / Thomas, L. / Adams, D.J. / Lewis, R.J. / Craik, D.J.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu-O-conotoxin MrVIB


Theoretical massNumber of molelcules
Total (without water)3,4141
Polymers3,4141
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Mu-O-conotoxin MrVIB


Mass: 3414.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus marmoreus (invertebrata) / Secretion: venom / References: UniProt: Q26443
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
131E-COSY

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Sample preparation

DetailsContents: ~1 mM MrVIB / Solvent system: 50% CD3CN, 40% H2O, 10% D20
Sample conditionspH: 3.5 / Pressure: ambient / Temperature: 290 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
XEASY1.3.7Eccles, C.data analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 189 NOE-derived restraints, 15 dihedral angle restraints and 10 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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