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- PDB-2frb: NMR structure of the alpha-conotoxin GI (ASN4)-benzoylphenylalani... -

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Basic information

Entry
Database: PDB / ID: 2frb
TitleNMR structure of the alpha-conotoxin GI (ASN4)-benzoylphenylalanine derivative
ComponentsAlpha-conotoxin GIA
KeywordsTOXIN / ALPHA-CONOTOXIN GI / BENZOPHENONE ANALOGS / NICOTINIC ACETYLCHOLINE RECEPTOR ANTAGONIST
Function / homologyConotoxin, alpha-type / Alpha conotoxin precursor / Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / toxin activity / extracellular region / Alpha-conotoxin GI
Function and homology information
Biological speciesConus geographus (geography cone)
MethodSOLUTION NMR / simulated annealing
AuthorsPashkov, V.S. / Maslennikov, I. / Kasheverov, I.V. / Zhmak, M.N. / Utkin, Y.N. / Tsetlin, V.I. / Arseniev, A.S.
CitationJournal: Febs J. / Year: 2006
Title: Alpha-Conotoxin GI benzoylphenylalanine derivatives. (1)H-NMR structures and photoaffinity labeling of the Torpedo californica nicotinic acetylcholine receptor.
Authors: Kasheverov, I.E. / Chiara, D.C. / Zhmak, M.N. / Maslennikov, I.V. / Pashkov, V.S. / Arseniev, A.S. / Utkin, Y.N. / Cohen, J.B. / Tsetlin, V.I.
History
DepositionJan 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_entity_src_syn / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Alpha-conotoxin GIA


Theoretical massNumber of molelcules
Total (without water)1,5821
Polymers1,5821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINTS VIOLATION
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Alpha-conotoxin GIA


Mass: 1581.817 Da / Num. of mol.: 1 / Fragment: residues 1-13 / Source method: obtained synthetically / Details: The protein was chemically synthesized. / Source: (synth.) Conus geographus (geography cone) / References: UniProt: P01519

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
131ROESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON SYNTHETIC (PBF4)-GI ANALOGUE.

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Sample preparation

DetailsType: solution / Contents: 10 mM (Bpa4)-GI, 85% H2O/15% D2O / Label: sample_1 / Solvent system: 85% H2O/15% D2O
SampleConc.: 10 mM / Component: (Bpa4)-GI / Isotopic labeling: natural abundance
Sample conditionspH: 3.4 / Pressure: 1.0 atm / Temperature: 313.0 K

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Braun and Wuthrichrefinement
DYANA1.5Guntert, Braun and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: LEAST RESTRAINTS VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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