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- PDB-1dw5: NMR STRUCTURE OF OMEGA-CONOTOXIN MVIIA: NO CONSTRAINTS ON DISULPH... -

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Basic information

Entry
Database: PDB / ID: 1dw5
TitleNMR STRUCTURE OF OMEGA-CONOTOXIN MVIIA: NO CONSTRAINTS ON DISULPHIDE BRIDGES
ComponentsOMEGA-CONOTOXIN MVIIA
KeywordsTOXIN / CONOTOXIN / CALCIUM CHANNEL / CONFORMATIONAL EXCHANGE
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Conotoxin / Conotoxin
Similarity search - Domain/homology
Omega-conotoxin MVIIA
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsAtkinson, R.A. / Kieffer, B. / Dejaegere, A. / Sirockin, F. / Lefevre, J.-F.
CitationJournal: Biochemistry / Year: 2000
Title: Structural and dynamic characterization of omega-conotoxin MVIIA: the binding loop exhibits slow conformational exchange.
Authors: Atkinson, R.A. / Kieffer, B. / Dejaegere, A. / Sirockin, F. / Lefevre, J.F.
History
DepositionJan 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OMEGA-CONOTOXIN MVIIA


Theoretical massNumber of molelcules
Total (without water)2,6501
Polymers2,6501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 500structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide OMEGA-CONOTOXIN MVIIA


Mass: 2650.224 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN CONUS MAGUS (MAGUS CONE)
References: UniProt: P05484

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D COSY
1312D HOHAHA
1412D 13C-1H HSQC
NMR detailsText: TEMPERATURE DEPENDENCE OF CHEMICAL SHIFTS, NH EXCHANGE INTO D2O, RELAXATION MEASUREMENTS AT 500 AND 600 MHZ

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Sample preparation

DetailsContents: 1
Sample conditionsIonic strength: 0 / pH: 3.50 / Pressure: AMBIENT / Temperature: 283.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionClassification
XwinNMR1.2structure solution
Felix2.1structure solution
X-PLOR3.1structure solution
X-PLOR3.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SUBSTRUCTURE EMBEDDING BY DISTANCE GEOMETRY, SIMULATED ANNEALING REGULARISATION OF FULL STRUCTURE, SIMULATED ANNEALING REFINEMENT
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 25

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