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- PDB-2md6: NMR SOLUTION STRUCTURE OF ALPHA CONOTOXIN LO1A FROM Conus longurionis -

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Basic information

Entry
Database: PDB / ID: 2md6
TitleNMR SOLUTION STRUCTURE OF ALPHA CONOTOXIN LO1A FROM Conus longurionis
ComponentsALPHA CONOTOXIN LO1A
KeywordsTOXIN / CONOTOXIN / ALPHA CONOTOXIN
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature.
Similarity search - Domain/homology
Alpha-conotoxin Lo1a
Similarity search - Component
Biological speciesConus longurionis (invertebrata)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model5
AuthorsMaiti, M. / Lescrinier, E. / Herdewijn, P. / Lebbe, E.K.M. / Peigneur, S. / D'Souza, L. / Tytgat, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure-Function Elucidation of a New alpha-Conotoxin, Lo1a, from Conus longurionis.
Authors: Lebbe, E.K. / Peigneur, S. / Maiti, M. / Devi, P. / Ravichandran, S. / Lescrinier, E. / Ulens, C. / Waelkens, E. / D'Souza, L. / Herdewijn, P. / Tytgat, J.
History
DepositionSep 1, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: 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
A: ALPHA CONOTOXIN LO1A


Theoretical massNumber of molelcules
Total (without water)1,9371
Polymers1,9371
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)15 / 100STRUCTURES WITH THE LOWEST ENER
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ALPHA CONOTOXIN LO1A


Mass: 1937.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus longurionis (invertebrata) / References: UniProt: X1WB75*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 aliphatic
1512D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 2.6 mM CONOTOXIN LO1A, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.6 mM / Component: CONOTOXIN LO1A-1
Sample conditionsIonic strength: Not defined / pH: 5.9 / Pressure: 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 NIH2.25SCHWIETERS, KUSZEWSKI, TJrefinement
TopSpin2.1Brukerprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 190 / NOE intraresidue total count: 65 / NOE long range total count: 13 / NOE medium range total count: 46 / NOE sequential total count: 66 / Protein phi angle constraints total count: 8
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST ENER
Conformers calculated total number: 100 / Conformers submitted total number: 15

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