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- PDB-5jyh: Solution Structure of Hge36: Scorpine-like Peptide from Hadrurus ... -

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Basic information

Entry
Database: PDB / ID: 5jyh
TitleSolution Structure of Hge36: Scorpine-like Peptide from Hadrurus Gertschi
ComponentsHge-scorpine
KeywordsTOXIN / scorpine-like peptide / Hadrurus gertschi / antiparasitic activity
Function / homology
Function and homology information


potassium channel regulator activity / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Long chain scorpion toxin family / Potassium channel toxin / BetaSPN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile.
Similarity search - Domain/homology
Biological speciesHadrurus gertschi (scorpion)
MethodSOLUTION NMR / molecular dynamics
AuthorsFlores-Solis, D. / Rodriguez De La Vega, R. / del Rio-Portilla, F.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)166472 Mexico
DGAPA-UNAMIN207713 Mexico
CitationJournal: Febs Lett. / Year: 2016
Title: Solution structure and antiparasitic activity of scorpine-like peptides from Hoffmannihadrurus gertschi.
Authors: Flores-Solis, D. / Toledano, Y. / Rodriguez-Lima, O. / Cano-Sanchez, P. / Ramirez-Cordero, B.E. / Landa, A. / Rodriguez de la Vega, R.C. / Del Rio-Portilla, F.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary
Category: citation / entity ...citation / entity / pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules ..._citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hge-scorpine


Theoretical massNumber of molelcules
Total (without water)4,8131
Polymers4,8131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Hge-scorpine / Hg-scorpine-like 1 / Hgscplike1


Mass: 4812.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadrurus gertschi (scorpion) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0GY40

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic22D 1H-1H TOCSY
131isotropic22D DQF-COSY
141isotropic22D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 3.0 mM HgeD, 95% H2O/5% D2O / Label: HgeD / Solvent system: 95% H2O/5% D2O
SampleConc.: 3.0 mM / Component: HgeD / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 Not defined / Label: Std_conditions / pH: 3.5 / Pressure: 0.98 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: chiral restrains added
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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