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- PDB-2jtb: Three dimensional solution structure of hainantoxin-III by 2D 1H-NMR -

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Basic information

Entry
Database: PDB / ID: 2jtb
TitleThree dimensional solution structure of hainantoxin-III by 2D 1H-NMR
ComponentsHainantoxin-3
KeywordsTOXIN / hainantoxin-III / spider toxin / Amidation / Ionic channel inhibitor / Knottin / Neurotoxin / Presynaptic neurotoxin / Secreted / Sodium channel inhibitor
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
Hainantoxin-III 1 / Hainantoxin-III 6
Similarity search - Component
Biological speciesOrnithoctonus hainana (spider)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsZhu, Q. / Liu, Z. / Liang, S.
CitationJournal: To be Published
Title: Three dimensional solution structure of hainantoxin-III by 2D 1H-NMR
Authors: Zhu, Q. / Liu, Z. / Liang, S.
History
DepositionJul 25, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hainantoxin-3


Theoretical massNumber of molelcules
Total (without water)3,6211
Polymers3,6211
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)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Hainantoxin-3 / Hainantoxin-III / HnTx-III


Mass: 3621.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ornithoctonus hainana (spider) / References: UniProt: P83464, UniProt: D2Y1X9*PLUS
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 5 mM entity_2, 25 mM [U-99% 2H] sodium acetate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMentity_21
25 mMsodium acetate[U-99% 2H]1
Sample conditionsIonic strength: 25 / pH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: X-PLOR / Classification: refinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
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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