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- PDB-2roo: Solution structure of Magi4, a spider toxin from Macrothele gigas -

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Basic information

Entry
Database: PDB / ID: 2roo
TitleSolution structure of Magi4, a spider toxin from Macrothele gigas
ComponentsNeurotoxin magi-4
KeywordsTOXIN / spider / sodium channel inhibitor / Cleavage on pair of basic residues / Ionic channel inhibitor / Knottin / Neurotoxin / Secreted
Function / homology
Function and homology information


sodium channel inhibitor activity / : / toxin activity / extracellular region
Similarity search - Function
Atracotoxin, delta / Delta Atracotoxin / Delta-atracotoxin (ACTX) family signature. / Omega-AgatoxinV - #10 / Omega-AgatoxinV / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Delta-hexatoxin-Mg1a
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsYamaji, N.
CitationJournal: To be Published
Title: Chemical synthesis and solution structure of a spider toxin that affects the inactivation of mammalian sodium channels
Authors: Yamaji, N. / Nishio, H. / Villegas, E. / Nishiuchi, Y. / Corzo, G.
History
DepositionApr 4, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurotoxin magi-4


Theoretical massNumber of molelcules
Total (without water)5,1661
Polymers5,1661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neurotoxin magi-4


Mass: 5165.951 Da / Num. of mol.: 1 / Fragment: Neurotoxin magi-4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P83560

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D DQF-COSY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY

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Sample preparation

DetailsContents: 3.7 mM magi4, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.7 mM / Component: magi4
Sample conditionspH: 2.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.9.1Schwieters, Kuszewski, Tjandra and Clorestructure solution
ANSIG3.3Kraulischemical shift assignment
ANSIG3.3Kraulispeak picking
XwinNMR2.5Bruker Biospincollection
XwinNMR2.5Bruker Biospinprocessing
X-PLOR NIH2.9.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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