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- PDB-7ay8: NMR solution structure of Tbo-IT2 -

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Basic information

Entry
Database: PDB / ID: 7ay8
TitleNMR solution structure of Tbo-IT2
ComponentsTbo-IT2
KeywordsTOXIN / PROTEIN
Biological speciesTibellus oblongus (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsMineev, K.S. / Kornilov, F.D. / Lushpa, V.A. / Korolkova, Y.A. / Maleeva, E.E. / Andreev, Y.A. / Kozlov, S.A. / Arseniev, A.S.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30014 Russian Federation
Russian Foundation for Basic Research18-04-00994A Russian Federation
CitationJournal: Toxins / Year: 2021
Title: New Insectotoxin from Tibellus Oblongus Spider Venom Presents Novel Adaptation of ICK Fold.
Authors: Korolkova, Y. / Maleeva, E. / Mikov, A. / Lobas, A. / Solovyeva, E. / Gorshkov, M. / Andreev, Y. / Peigneur, S. / Tytgat, J. / Kornilov, F. / Lushpa, V. / Mineev, K. / Kozlov, S.
History
DepositionNov 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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: Tbo-IT2


Theoretical massNumber of molelcules
Total (without water)4,2211
Polymers4,2211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Tbo-IT2


Mass: 4220.974 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tibellus oblongus (spider) / Plasmid: pET32b+ / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-15N HSQC
251isotropic12D 1H-1H COSY
261isotropic12D 1H-1H NOESY
271isotropic12D 1H-13C HSQC aliphatic
281isotropic12D 1H-1H TOCSY
NMR detailsText: NULL

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Sample preparation

DetailsType: solution / Contents: 1.3 mM peptide, 95% H2O/5% D2O / Label: main_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.3 mM / Component: peptide / Isotopic labeling: natural abundance
Sample conditions

Ionic strength: 0 Not defined / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 303 K

Conditions-IDLabelpHDetails
1main_condition3.0
2second_condition3.0 pDpure D2O

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert P.structure calculation
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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