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- PDB-2ifi: Ala6 Variant of ImI Conotoxin -

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Basic information

Entry
Database: PDB / ID: 2ifi
TitleAla6 Variant of ImI Conotoxin
ComponentsAlpha-conotoxin ImI
KeywordsTOXIN / Conotoxin / disulfide linkages / ribbon conformation
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / Energy minimization, Molecular dynamics, Simulated annealing
Model type detailsminimized average
AuthorsKini, R.M. / Kang, T.S.
CitationJournal: Biochemistry / Year: 2007
Title: Protein folding determinants: structural features determining alternative disulfide pairing in alpha- and chi/lambda-conotoxins
Authors: Kang, T.S. / Talley, T.T. / Jois, S.D. / Taylor, P. / Kini, R.M.
History
DepositionSep 21, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_nmr_software ...pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref / struct_ref_seq
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-conotoxin ImI


Theoretical massNumber of molelcules
Total (without water)1,3311
Polymers1,3311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint0 kcal/mol
Surface area1320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Alpha-conotoxin ImI


Mass: 1330.564 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized by Fmoc solid phase peptide synthesis.
Source: (synth.) synthetic construct (others) / Keywords: P6A
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D ROESY

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Sample preparation

DetailsContents: 2mM peptide samples; 10% D2O, 90% H20 / Solvent system: 10% D2O, 90% H20
Sample conditionsIonic strength: 2mM / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
XwinNMRcollection
Mestre-C4.9.9.6processing
Discoverstructure solution
Discoverrefinement
RefinementMethod: Energy minimization, Molecular dynamics, Simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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