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- PDB-7p4x: SOLUTION NMR STRUCTURE OF PALUSTRIN-CA IN 50% TRIFLUOROETHANOL -

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Basic information

Entry
Database: PDB / ID: 7p4x
TitleSOLUTION NMR STRUCTURE OF PALUSTRIN-CA IN 50% TRIFLUOROETHANOL
ComponentsPalustrin-Ca antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / Palustrin-Ca / antimicrobial peptide / anticancer peptide / alpha helix
Function / homology
Function and homology information


other organism cell membrane / defense response to bacterium / innate immune response / extracellular region / membrane
Similarity search - Function
Frog antimicrobial peptide, brevinin-2/esculentin type / Frog antimicrobial peptide / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide
Similarity search - Domain/homology
Biological speciesLithobates catesbeianus (American bullfrog)
MethodSOLUTION NMR / simulated annealing
AuthorsTimmons, P.B. / Hewage, C.M.
CitationJournal: Sci Rep / Year: 2021
Title: Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca.
Authors: Timmons, P.B. / Hewage, C.M.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 23, 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: Palustrin-Ca antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)3,3091
Polymers3,3091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2900 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Palustrin-Ca antimicrobial peptide


Mass: 3308.974 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lithobates catesbeianus (American bullfrog)
References: UniProt: C5IB04
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
111anisotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-13C HSQC
141anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 2.27 mM NA- Palustrin-Ca, trifluoroethanol/water / Label: sample / Solvent system: trifluoroethanol/water
SampleConc.: 2.27 mM / Component: Palustrin-Ca / Isotopic labeling: NA-
Sample conditionsIonic strength: 0 Not defined / Label: conditions / pH: 7.0 Not defined / 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 Biospinprocessing
NMRFAM-SPARKYNational Magnetic Resonance Facility at Madisonpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NAMDNIH CENTER FOR MACROMOLECULAR MODELING & BIOINFORMATICS UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGNrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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