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- PDB-6wpb: NMR Structure of HSP1-NH2 antimicrobial peptide in presence of SD... -

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Basic information

Entry
Database: PDB / ID: 6wpb
TitleNMR Structure of HSP1-NH2 antimicrobial peptide in presence of SDS-d25 micelles
ComponentsHSP1-NH2
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Hylaseptin-P1
Function and homology information
Biological speciesBoana punctata (polka-dot treefrog)
MethodSOLUTION NMR / simulated annealing
AuthorsVerly, R.M. / Gomes, I.P.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2020
Title: Membrane interactions of the anuran antimicrobial peptide HSP1-NH2: Different aspects of the association to anionic and zwitterionic biomimetic systems.
Authors: Gomes, I.P. / Santos, T.L. / de Souza, A.N. / Nunes, L.O. / Cardoso, G.A. / Matos, C.O. / Costa, L.M.F. / Liao, L.M. / Resende, J.M. / Verly, R.M.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HSP1-NH2


Theoretical massNumber of molelcules
Total (without water)1,3121
Polymers1,3121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide HSP1-NH2


Mass: 1311.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Boana punctata (polka-dot treefrog) / References: UniProt: P84292
Has ligand of interestY
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
131isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

DetailsType: micelle / Contents: 1 mM unlable HSP-1, 90% H2O/10% D2O / Details: 200 mM SDS-d25 micelles / Label: natural abundace / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: HSP-1 / Isotopic labeling: unlable
Sample conditionsDetails: 200 mM SDS-d25 micelles / Ionic strength: undifined Not defined / Label: SDS-d25 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Bruker Avance III / Manufacturer: Bruker / Model: Bruker Avance III / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
QUEENNabuurs, Spronk, Krieger, Maassen, Vriend and Vuisterdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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