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- PDB-1r9i: NMR Solution Structure of PIIIA toxin, NMR, 20 structures -

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Basic information

Entry
Database: PDB / ID: 1r9i
TitleNMR Solution Structure of PIIIA toxin, NMR, 20 structures
ComponentsMu-conotoxin PIIIA
KeywordsTOXIN / Conotoxin / Cysteine knot
Function / homologyConotoxin, mu-type / Mu-conotoxin family signature. / Conotoxin / Conotoxin / sodium channel inhibitor activity / : / toxin activity / extracellular region / Mu-conotoxin PIIIA
Function and homology information
Biological speciesConus purpurascens (invertebrata)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsNielsen, K.J. / Watson, M. / Adams, D.J. / Hammarstrom, A.K. / Gage, P.W. / Hill, J.M. / Craik, D.J. / Thomas, L. / Adams, D. / Alewood, P.F. / Lewis, R.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Solution structure of mu-conotoxin PIIIA, a preferential inhibitor of persistent tetrodotoxin-sensitive sodium channels
Authors: Nielsen, K.J. / Watson, M. / Adams, D.J. / Hammarstrom, A.K. / Gage, P.W. / Hill, J.M. / Craik, D.J. / Thomas, L. / Adams, D. / Alewood, P.F. / Lewis, R.J.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_assembly ...entity_poly / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu-conotoxin PIIIA


Theoretical massNumber of molelcules
Total (without water)2,6181
Polymers2,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area260 Å2
ΔGint-3 kcal/mol
Surface area2070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein/peptide Mu-conotoxin PIIIA


Mass: 2618.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus purpurascens (invertebrata) / References: UniProt: P58925

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
242E-COSY
2522D NOESY
2622D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM PIIIA, 95% H2O, 5% D2O95% H2O/5% D2O
22mM PIIIA, 100% D2O100% D2O
Sample conditions
Conditions-IDpHTemperature (K)
13.0 298 K
25.5 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRcollection
AURELIAprocessing
UXNMRprocessing
X-PLOR3.8Brunger, A.T.structure solution
X-PLOR3.8refinement
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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