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- PDB-1y29: Three dimensional solution structure of huwentoxin-x by 2D 1H-NMR -

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Basic information

Entry
Database: PDB / ID: 1y29
TitleThree dimensional solution structure of huwentoxin-x by 2D 1H-NMR
Componentshuwentoxin-x
KeywordsTOXIN / A double-stranded beta-sheet / ICK / Knottin
Function / homologycalcium channel regulator activity / toxin activity / extracellular region / Omega-theraphotoxin-Hs1a
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLiu, Z. / Liang, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Function and solution structure of Huwentoxin-X, a specific blocker of N-type calcium channels, from the Chinese bird spider Ornithoctonus huwena
Authors: Liu, Z. / Dai, J. / Dai, L. / Deng, M. / Hu, Z. / Hu, W. / Liang, S.
History
DepositionNov 22, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units
Revision 1.4Oct 30, 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: huwentoxin-x


Theoretical massNumber of molelcules
Total (without water)2,9431
Polymers2,9431
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 / 100structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein/peptide huwentoxin-x


Mass: 2942.567 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was isolated from the venom of spider Ornithoctonus huwena, synthesized by using solid phase chemical method.
References: UniProt: P68424
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: 5MM HUWENTOXIN-X; PHOSPHATE BUFFER / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 / pH: 4.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5Bruce A. Johnsondata analysis
X-PLORNIH-2.9.6C.D. Schwietersrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on 261 noe-derived distance constraints, 10 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: 100 / Conformers submitted total number: 20

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