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- PDB-1kqi: NMR Solution Structure of the trans Pro30 Isomer of ACTX-Hi:OB4219 -

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Basic information

Entry
Database: PDB / ID: 1kqi
TitleNMR Solution Structure of the trans Pro30 Isomer of ACTX-Hi:OB4219
ComponentsACTX-Hi:OB4219
KeywordsTOXIN / Hadronyche infensa / funnel web / spider venom / cis-trans isomerisation / disulfide rich / cystine knot / solution structure / NMR spectroscopy
Function / homologyBeta/delta-agatoxin family / Mu-agatoxin family signature. / sodium channel regulator activity / toxin activity / extracellular region / U2-hexatoxin-Hi1a
Function and homology information
Biological speciesHadronyche infensa (spider)
MethodSOLUTION NMR / Torsion angle dynamics. Refinement, energy minimization in a water shell using Cartesian dynamics, powell minimization.
AuthorsRosengren, K.J. / Wilson, D. / Daly, N.L. / Alewood, P.F. / Craik, D.J.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structures of the cis- and trans-Pro30 isomers of a novel 38-residue toxin from the venom of Hadronyche Infensa sp. that contains a cystine-knot motif within its four disulfide bonds
Authors: Rosengren, K.J. / Wilson, D. / Daly, N.L. / Alewood, P.F. / Craik, D.J.
History
DepositionJan 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Revision 1.4Oct 16, 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: ACTX-Hi:OB4219


Theoretical massNumber of molelcules
Total (without water)4,2311
Polymers4,2311
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 least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACTX-Hi:OB4219


Mass: 4230.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Hadronyche infensa found at Orchid Beach, Fraser Island, Australia
Source: (natural) Hadronyche infensa (spider) / References: UniProt: P60272*PLUS
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
121NOESY
131TOCSY
142E-COSY
152NOESY
162TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mg ACTX-Hi:OB42190.5 ml 80% H2O/10% D2O/10% CH3CN
23mg ACTX-Hi:OB42190.5 ml 90% D2O/10% CH3CN
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 mM 5ambient 298 K
20 mM 5ambient 293 K
30 mM 5ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3.7Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
CNS1Brunger, A.T. et al.structure solution
ARIA1Linge, J.P., O'Donoghue, S.I., Nilges, M.N.refinement
RefinementMethod: Torsion angle dynamics. Refinement, energy minimization in a water shell using Cartesian dynamics, powell minimization.
Software ordinal: 1
Details: Initial structures were generated by torsion angle dynamics. These were then refined and minimized in a water shell using Cartesian dynamics and restrained powell minimization according to ...Details: Initial structures were generated by torsion angle dynamics. These were then refined and minimized in a water shell using Cartesian dynamics and restrained powell minimization according to ARIA and CNS protocols.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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