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- PDB-2ncx: Solution structure of pseudin-2 isolated from the skin of paradox... -

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Basic information

Entry
Database: PDB / ID: 2ncx
TitleSolution structure of pseudin-2 isolated from the skin of paradoxical frog, Pseudis paradoxa
ComponentsPseudin-2
KeywordsANTIMICROBIAL PROTEIN / pseudin-2
Function / homologyPseudin antimicrobial peptide / Pseudin antimicrobial peptide / defense response to fungus / xenobiotic metabolic process / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Pseudin-2
Function and homology information
Biological speciesPseudis paradoxa (paradox frog)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsJeon, D. / Kim, J. / Shin, A. / Kim, Y.
CitationJournal: To be Published
Title: Optimum Balance between the Cationicity and Structural Component for Bacterial Cell Selectivity and Anti-inflammatory activities of Pseudin-2 and its Analogs
Authors: Jeon, D. / Kim, J. / Lee, E. / Bang, J. / Kim, Y.
History
DepositionApr 18, 2016Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: Pseudin-2


Theoretical massNumber of molelcules
Total (without water)2,6901
Polymers2,6901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pseudin-2


Mass: 2690.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudis paradoxa (paradox frog) / References: UniProt: P83189

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY

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Sample preparation

DetailsContents: 200 mM DPC-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 200 mM / Component: DPC-1
Sample conditionsPressure: ambient / Temperature: 303

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, MUMENTHALER AND WUTHRICHrefinement
CYANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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