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- PDB-8xth: Thanatin PM15Y in LPS -

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Basic information

Entry
Database: PDB / ID: 8xth
TitleThanatin PM15Y in LPS
ComponentsThanatin
KeywordsANTIMICROBIAL PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Thanatin
Function and homology information
Biological speciesPodisus maculiventris (spined soldier bug)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSwaleeha, A. / Bhattacharrya, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Thanatin VF16QK in LPS
Authors: Swaleeha, A. / Bhattacharrya, S.
History
DepositionJan 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thanatin


Theoretical massNumber of molelcules
Total (without water)1,9091
Polymers1,9091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Thanatin


Mass: 1909.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Podisus maculiventris (spined soldier bug) / References: UniProt: P55788

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY

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Sample preparation

DetailsType: solution / Contents: 300 uM Thanatin PM15Y in LPS, 90% H2O/10% D2O / Label: Thanatin PM15Y in LPS / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: Thanatin PM15Y in LPS / Isotopic labeling: none
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 5 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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