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- PDB-1mb6: Three dimensional solution structure of huwentoxin-IV by 2D 1H-NMR -

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Basic information

Entry
Database: PDB / ID: 1mb6
TitleThree dimensional solution structure of huwentoxin-IV by 2D 1H-NMR
Componentshuwentoxin-iv
KeywordsTOXIN / containing a double-stranded beta-sheet and four beta-turns
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Huwentoxin, conserved site-1 / Huwentoxin-1 family signature. / Huwentoxin-1 family / Ion channel inhibitory toxin
Similarity search - Domain/homology
Biological speciesOrnithoctonus huwena (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
AuthorsPeng, K. / Shu, Q. / Liang, S.P.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Function and solution structure of huwentoxin-IV, a potent neuronal tetrodotoxin (TTX)-sensitive sodium channel antagonist from Chinese bird spider Selenocosmia huwena
Authors: Peng, K. / Shu, Q. / Liu, Z. / Liang, S.P.
History
DepositionAug 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 1.4Oct 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 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: huwentoxin-iv


Theoretical massNumber of molelcules
Total (without water)4,1211
Polymers4,1211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide huwentoxin-iv


Mass: 4120.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Ornithoctonus huwena (Chinese earth tiger)
Secretion: venom / References: UniProt: P83303
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141E-COSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

DetailsContents: 5MM HUWENTOXIN-IV MMOL/L PHOSPHATE BUFFER; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 / pH: 4.5 / Pressure: 1 atm / Temperature: 300.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felix98MSI.Corp.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 527 NOE-DERIVED DISTANCE CONSTRAINTS, 14 DIHEDRAL ANGEL RESTRAINTS AND 9 FAKE DISTANCE RESTRAINTS FROM DISULFIDE BONDS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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