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- PDB-2lds: Solution Structure of a Short-chain LaIT1 from the Venom of Scorp... -

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Basic information

Entry
Database: PDB / ID: 2lds
TitleSolution Structure of a Short-chain LaIT1 from the Venom of Scorpion Liocheles australasiae
ComponentsInsecticidal toxin LaIT1
KeywordsTOXIN / Inhibitor Cystine Knot (ICK) fold / scorpion toxin
Function / homologytoxin activity / extracellular region / Insecticidal toxin LaIT1
Function and homology information
Biological speciesLiocheles australasiae (scorpion)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHorita, S. / Miyakawa, T. / Nagata, K. / Tanokura, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Solution structure of a short-chain insecticidal toxin LaIT1 from the venom of scorpion Liocheles australasiae.
Authors: Horita, S. / Matsushita, N. / Kawachi, T. / Ayabe, R. / Miyashita, M. / Miyakawa, T. / Nakagawa, Y. / Nagata, K. / Miyagawa, H. / Tanokura, M.
History
DepositionJun 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Structure summary
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insecticidal toxin LaIT1


Theoretical massNumber of molelcules
Total (without water)4,2151
Polymers4,2151
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Insecticidal toxin LaIT1


Mass: 4214.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liocheles australasiae (scorpion) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C5F2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CO)CA
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11112D 1H-13C HSQC

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Sample preparation

DetailsContents: 90% H2O-1, 10% D2O-2, 20mM MES-3, 50mM sodium chloride-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
90 %H2O-11
10 %D2O-21
20 mMMES-31
50 mMsodium chloride-41
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANAv2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 303 / NOE intraresidue total count: 57 / NOE long range total count: 76 / NOE medium range total count: 54 / NOE sequential total count: 112
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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