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- PDB-6afq: Thanatin M21F in presence of DPC -

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Basic information

Entry
Database: PDB / ID: 6afq
TitleThanatin M21F in presence of DPC
ComponentsThanatin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / thanatin
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
AuthorsBhattacharjya, S. / Sinha, S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: To Be Published
Title: Thanatin M21F in presence of DPC
Authors: Bhattacharjya, S. / Sinha, S.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: 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
Revision 1.2Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)2,4581
Polymers2,4581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2540 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: 2457.962 Da / Num. of mol.: 1 / Mutation: M21F / 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 NOESY
121isotropic12D TOCSY

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Sample preparation

DetailsType: solution / Contents: 0.3 mM 1H ThanatinM21F, 90% H2O/10% D2O / Label: sample_1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: ThanatinM21F / Isotopic labeling: 1H
Sample conditionsIonic strength: 125 mM / Label: conditions_1 / pH: 5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
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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