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- PDB-8w16: Pyroglutamaic acid position 1 synthetic analogue of RgIA -

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Basic information

Entry
Database: PDB / ID: 8w16
TitlePyroglutamaic acid position 1 synthetic analogue of RgIA
ComponentsAlpha-conotoxin RgIA
KeywordsSTRUCTURAL PROTEIN
Function / homologyConotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region / Alpha-conotoxin RgIA
Function and homology information
Biological speciesConus regius (invertebrata)
MethodSOLUTION NMR / na
AuthorsAgwa, A.J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To Be Published
Title: On-resin bicyclization improves synthesis of alpha-conotoxin RgIA4-6
Authors: Giribaldi, J. / Agwa, A.J. / Schroeder, C.I.
History
DepositionFeb 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin RgIA


Theoretical massNumber of molelcules
Total (without water)1,9361
Polymers1,9361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, Assembly of PCA not rendering correctly
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Alpha-conotoxin RgIA


Mass: 1935.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Conus regius (invertebrata) / References: UniProt: P0C1D0
Has ligand of interestY
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
112anisotropic12D 1H-13C HSQC
121anisotropic12D 1H-15N HSQC
131anisotropic12D 1H-1H NOESY
141anisotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mg/mL JG055, 90% H2O/10% D2OJG05590% H2O/10% D2O
solution21 mg/mL JG055, 100% D2OJG055-D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mLJG055natural abundance1
1 mg/mLJG055natural abundance2
Sample conditionsIonic strength: na M / Label: JG055 / pH: 4 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 2 / Details: no refinement was performed
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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