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- PDB-2b5q: Solution structure of globular conformation of CMrVIA lambda conotoxin -

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Basic information

Entry
Database: PDB / ID: 2b5q
TitleSolution structure of globular conformation of CMrVIA lambda conotoxin
ComponentsLambda-conotoxin CMrVIA
KeywordsTOXIN / conotoxin / disulfide linkage / ribbon conformation
Function / homologytoxin activity / extracellular region / Chi-conotoxin CMrVIA
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, energy minimization
Model type detailsminimized average
AuthorsKang, T.S. / Jois, S.D.S. / Kini, R.M.
CitationJournal: Biomacromolecules / Year: 2006
Title: Solution Structures of Two Structural Isoforms of CMrVIA chi/lambda-Conotoxin
Authors: Kang, T.S. / Jois, S.D.S. / Kini, R.M.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lambda-conotoxin CMrVIA


Theoretical massNumber of molelcules
Total (without water)1,2441
Polymers1,2441
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 / 211structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Lambda-conotoxin CMrVIA


Mass: 1243.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized using Fmoc-Chemistry Solid Phase Peptide synthesis. The sequence of the peptide is naturally found in Conus marmoreus (Marble cone).
References: UniProt: P58807

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
121DQF-COSY
1312D ROESY

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Sample preparation

DetailsContents: 3mM peptide sample; 10% D20, 90% H20 / Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 3mM / pH: 3 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRcollection
Mestre-C4.5.9processing
Insight IIstructure solution
Insight IIACCELRYSrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, energy minimization
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 211 / Conformers submitted total number: 15

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