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- PDB-5xok: Thanatin Y10M21AA in complex with LPS -

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Basic information

Entry
Database: PDB / ID: 5xok
TitleThanatin Y10M21AA in complex with LPS
ComponentsThanatin
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide
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 / na
AuthorsSinha, S. / Bhattacharjya, S.
CitationJournal: To Be Published
Title: Thanatin Y10M21AA in complex with LPS
Authors: Sinha, S. / Bhattacharjya, S.
History
DepositionMay 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thanatin
B: Thanatin


Theoretical massNumber of molelcules
Total (without water)4,5802
Polymers4,5802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area670 Å2
ΔGint-8 kcal/mol
Surface area3680 Å2
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: 2289.770 Da / Num. of mol.: 2 / Mutation: Y10A, M21A / Source method: obtained synthetically / Source: (synth.) Podisus maculiventris (spined soldier bug) / References: UniProt: P55788
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
111isotropic12D tr-NOESY
121isotropic12D TOCSY

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Sample preparation

DetailsType: solution / Contents: 400 uM Thanatin Y10M21AA, 90% H2O/10% D2O / Label: Thanatin Y10M21AA-LPS / Solvent system: 90% H2O/10% D2O
SampleConc.: 400 uM / Component: Thanatin Y10M21AA / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 5 / Pressure: 1 atm / Temperature: 298 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
TopSpinBruker Biospindata analysis
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: na / Software ordinal: 3
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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