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- PDB-1wqb: Three-dimensional Solution Strucutre of Aptotoxin VII, from the v... -

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Basic information

Entry
Database: PDB / ID: 1wqb
TitleThree-dimensional Solution Strucutre of Aptotoxin VII, from the venom of a Trap-door Spider
ComponentsAptotoxin VII
KeywordsTOXIN / spider's venom / cystein framework / cystine knot motif
Function / homologytoxin activity / extracellular region / U3-cyrtautoxin-As1a
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsKobayashi, K. / Kim, J.-I. / Sato, K. / Kohno, T.
CitationJournal: To be Published
Title: Three-dimensional Solution Structure of Aptotoxin VII, from the Venom of a Trap-door Spider
Authors: Kobayashi, K. / Kim, J.-I. / Sato, K. / Kohno, T.
History
DepositionSep 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: 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
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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:
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Assembly

Deposited unit
A: Aptotoxin VII


Theoretical massNumber of molelcules
Total (without water)3,5411
Polymers3,5411
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)18 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Aptotoxin VII / Paralytic peptide VII / PP VII


Mass: 3541.068 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chamically synthesized. This sequence occurs naturally in Aptostichus schlingeri.
References: UniProt: P49271
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
1422D NOESY
1522D TOCSY
162PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM Aptotoxin; 90% H2O, 10% D2O90% H2O/10% D2O
210mM Aptotoxin; D2OD2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR96Brukercollection
UXNMR96Brukerprocessing
X-PLOR3.1refinement
X-PLOR3.1Brungerstructure solution
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 392 restraints, 358 are NOE-derived distance constraints, 19 dihedral angle restraints, 15 distance restraints from hydrogen bonds and disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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