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- PDB-2lu6: NMR solution structure of Midi peptide designed based on m-conotoxins -

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Basic information

Entry
Database: PDB / ID: 2lu6
TitleNMR solution structure of Midi peptide designed based on m-conotoxins
ComponentsMidi peptide designed based on m-conotoxins
KeywordsDE NOVO PROTEIN / TOXIN / m-conotoxin / KIIIA / BuIIIC
Function / homologyConotoxin / Conotoxin / ion channel inhibitor activity / : / toxin activity / extracellular region / Mu-conotoxin BuIIIC
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDyubankova, N. / Lescrinier, E. / Stevens, M. / Tytgat, J. / Herdewijn, P. / Peigneur, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Design of bioactive peptides from naturally occurring mu-conotoxin structures.
Authors: Stevens, M. / Peigneur, S. / Dyubankova, N. / Lescrinier, E. / Herdewijn, P. / Tytgat, J.
History
DepositionJun 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Midi peptide designed based on m-conotoxins


Theoretical massNumber of molelcules
Total (without water)1,7011
Polymers1,7011
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Midi peptide designed based on m-conotoxins


Mass: 1700.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: C1J5M7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1412D 1H-13C HSQC
1512D 1H-13C HSQC-TOCSY

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Sample preparation

DetailsContents: 2 mM mM protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.0 mM / Component: entity-1
Sample conditionsPressure: ambient / Temperature: 278 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 software
NameVersionDeveloperClassification
X-PLOR NIH3.851Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 179 / NOE intraresidue total count: 128 / NOE long range total count: 7 / NOE medium range total count: 10 / NOE sequential total count: 34
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 19

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