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- PDB-2n7f: NMR solution structure of muO-conotoxin MfVIA -

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Basic information

Entry
Database: PDB / ID: 2n7f
TitleNMR solution structure of muO-conotoxin MfVIA
ComponentsmuO-conotoxin MfVIA
KeywordsTOXIN / muO-conotoxin / diulfide-rich
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsSchroeder, C.I. / Mobli, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Development of a mu O-Conotoxin Analogue with Improved Lipid Membrane Interactions and Potency for the Analgesic Sodium Channel NaV1.8.
Authors: Deuis, J.R. / Dekan, Z. / Inserra, M.C. / Lee, T.H. / Aguilar, M.I. / Craik, D.J. / Lewis, R.J. / Alewood, P.F. / Mobli, M. / Schroeder, C.I. / Henriques, S.T. / Vetter, I.
History
DepositionSep 9, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.5Oct 30, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: muO-conotoxin MfVIA


Theoretical massNumber of molelcules
Total (without water)3,6561
Polymers3,6561
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 muO-conotoxin MfVIA


Mass: 3656.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1513D 13C HSQC-NOESY

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Sample preparation

DetailsContents: 10 mM MfVIA, 70% H2O/30% CD3CN / Solvent system: 70% H2O/30% CD3CN
SampleConc.: 10 mM / Component: MfVIA-1
Sample conditionsPressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichpeak picking
CYANA3Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichchemical shift calculation
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.chemical shift calculation
XEASYBartels et al.peak picking
XEASYBartels et al.structure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 438 / NOE intraresidue total count: 117 / NOE long range total count: 128 / NOE medium range total count: 34 / NOE sequential total count: 159
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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