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- PDB-2lmz: Solution NMR structure of the novel conotoxin im23a from Conus im... -

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Basic information

Entry
Database: PDB / ID: 2lmz
TitleSolution NMR structure of the novel conotoxin im23a from Conus imperialis
ComponentsConotoxin im17a
KeywordsTOXIN / conotoxin / novel / helix / hairpin / Conus imperialis
Function / homologyArc Repressor Mutant, subunit A - #2920 / toxin activity / Arc Repressor Mutant, subunit A / Orthogonal Bundle / extracellular region / Mainly Alpha / Conotoxin im23a
Function and homology information
Biological speciesConus imperialis (invertebrata)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 19
AuthorsKhoo, K.K. / Galea, C.A. / Boonyalai, N. / Norton, R.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: A helical conotoxin from Conus imperialis has a novel cysteine framework and defines a new superfamily.
Authors: Ye, M. / Khoo, K.K. / Xu, S. / Zhou, M. / Boonyalai, N. / Perugini, M.A. / Shao, X. / Chi, C. / Galea, C.A. / Wang, C. / Norton, R.S.
History
DepositionDec 15, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_nmr_software ...citation / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conotoxin im17a


Theoretical massNumber of molelcules
Total (without water)4,8351
Polymers4,8351
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3350 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Conotoxin im17a


Mass: 4834.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus imperialis (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: D0PX84

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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 DQF-COSY
1512D 1H-1H NOESY
1613D 1H-15N NOESY
1722D 1H-1H TOCSY
1822D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1128 uM [U-15N] Conotoxin-1, 95% H2O/5% D2O95% H2O/5% D2O
2128 uM Conotoxin-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
128 uMConotoxin-1[U-15N]1
128 uMConotoxin-22
Sample conditionspH: 5.6 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.processing
XEASYBartels et al.peak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 19

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