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- PDB-7wkf: Antimicrobial peptide-LaIT2 -

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Basic information

Entry
Database: PDB / ID: 7wkf
TitleAntimicrobial peptide-LaIT2
ComponentsBeta-KTx-like peptide LaIT2
KeywordsSTRUCTURAL PROTEIN / CYANA 2.1 Scorpion Antimicrobial peptide
Function / homologyLong chain scorpion toxin family / Long chain scorpion toxin, cysteine-stabilized alpha/beta domain / BetaSPN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / toxin activity / defense response to bacterium / extracellular region / Peptide LaIT2
Function and homology information
Biological speciesLiocheles australasiae (scorpion)
MethodSOLUTION NMR / simulaed annealing
AuthorsTamura, M. / Morita, H. / Ohki, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Toxicon / Year: 2022
Title: Structural and functional studies of LaIT2, an antimicrobial and insecticidal peptide from Liocheles australasiae.
Authors: Tamura, M. / Tatsushiro, C. / Morita, E.H. / Ohki, S.
#1: Journal: Biosci. Biotechnol. Biochem / Year: 2009
Title: Purification and cDNA cloning of LaIT2, a novel insecticidal toxin from venom of the scorpion Liocheles australasiae
Authors: Matsushita, M.N. / Miyashita, M.M. / Ichiki, I.Y. / Ogura, O.T. / Sakuradani, S.E. / Nakagawa, N.Y. / Shimizu, S.S. / Miyagawa, M.H.
#2: Journal: J. Pept. Sci / Year: 2018
Title: Chemical synthesis of a two-domain scorpion toxin LaIT2 and its single-domain analogs to elucidate structural factors important for insecticidal and antimicrobial activities
Authors: Juichi, H.J. / Ando, A.R. / Ishido, I.T. / Miyashita, M.M. / Ogura, O.T. / Sakuradani, S.E. / Nakagawa, N.Y. / Miyagawa, M.H.
History
DepositionJan 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-KTx-like peptide LaIT2


Theoretical massNumber of molelcules
Total (without water)6,6511
Polymers6,6511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Beta-KTx-like peptide LaIT2


Mass: 6650.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liocheles australasiae (scorpion) / Plasmid: pET-mod / Production host: Escherichia coli (E. coli) / References: UniProt: C7G3K3
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D NOESY
132isotropic13D CBCA(CO)NH
142isotropic13D 1H-15N NOESY
152isotropic13D 1H-13C NOESY
162isotropic13D HNCA
192isotropic13D HN(CA)CB
182isotropic13D (H)CCH-TOCSY
172isotropic13D 1H-15N TOCSY
1132isotropic13D C(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.2 mM 15N LaIT2, 95% H2O/5% D2O15N_LaIT295% H2O/5% D2O
solution20.2 mM 13C LaIT2, 95% H2O/5% D2O13C_LaIT295% H2O/5% D2O
solution30.2 mM 13C/15N LaIT2, 95% H2O/5% D2O13C/15N_LaIT295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMLaIT215N1
0.2 mMLaIT213C2
0.2 mMLaIT213C/15N3
Sample conditionsIonic strength: 100 mM / Label: LaIT2 / pH: 6 / Pressure: 1.013 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
PONDEROSAWoonghee Leerefinement
MolProbityRichardsondata analysis
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
RefinementMethod: simulaed annealing / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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