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- PDB-1v5a: Solution Structure of Covalitoxin I -

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Basic information

Entry
Database: PDB / ID: 1v5a
TitleSolution Structure of Covalitoxin I
ComponentsCovalitoxin-I
KeywordsTOXIN / VENOM OF CORECNEMIUS VALIDUS / DISULFIDE BOND
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsKohno, T. / Sasaki, T. / Sato, K.
CitationJournal: To be Published
Title: Solution Structure of Covalitoxin I
Authors: Kohno, T. / Sasaki, T. / Sato, K.
History
DepositionNov 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Covalitoxin-I


Theoretical massNumber of molelcules
Total (without water)2,8181
Polymers2,8181
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)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Covalitoxin-I


Mass: 2818.434 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. This sequence occurs naturally in Coremiocnemis validus.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY
141PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 5mM Covalitoxin-I; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerdata analysis
X-PLOR3.1refinement
RefinementMethod: distance geometry, 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: 15

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