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- PDB-6bx9: Solution structure of conotoxin reg3b -

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Basic information

Entry
Database: PDB / ID: 6bx9
TitleSolution structure of conotoxin reg3b
ComponentsConotoxin
KeywordsTOXIN / mini-M / multi-turn scaffold
Function / homologytoxin activity / extracellular region / Conotoxin Reg3b
Function and homology information
Biological speciesConus regius (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsMari, F. / Dovell, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 066004 United States
Florida Sea Grant College ProgramR/LR-MB-18 United States
Florida Sea Grant College ProgramR/LR-MB-74 United States
CitationJournal: FEBS J. / Year: 2018
Title: Structural plasticity of mini-M conotoxins - expression of all mini-M subtypes by Conus regius.
Authors: Franco, A. / Dovell, S. / Moller, C. / Grandal, M. / Clark, E. / Mari, F.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 14, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_dist_value
Revision 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: Conotoxin


Theoretical massNumber of molelcules
Total (without water)1,6781
Polymers1,6781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Conotoxin / reg3b


Mass: 1678.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom duct / Source: (natural) Conus regius (invertebrata) / References: UniProt: P85021
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic1DQF-COSY
241isotropic12D 1H-1H NOESY
251isotropic12D 1H-1H TOCSY
361isotropic12D 1H-1H TOCSY
371isotropic12D 1H-1H NOESY
381isotropic11D 1H exchange

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Sample preparation

DetailsType: solution
Contents: 1.275 mM reg3b, 10 % [U-99% 2H] D2O, 0.025 mM TSP, 90 % H2O
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.275 mMreg3bnatural abundance1
10 %D2O[U-99% 2H]1
0.025 mMTSPnatural abundance1
90 %H2Onatural abundance1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1low-medium Not definedconditions_13.51 atm298 K
2low-medium Not definedconditions_23.51 atm273 K
3low-medium Not definedconditions_33.51 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVarianprocessing
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
AQUARullmann, Doreleijers and Kapteindata analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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