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- PDB-6twg: Solution structure of antimicrobial peptide, crabrolin Plus in th... -

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Basic information

Entry
Database: PDB / ID: 6twg
TitleSolution structure of antimicrobial peptide, crabrolin Plus in the presence of Lipopolysaccharide
ComponentsCrabrolin Plus, mutant of Crabrolin peptide
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide / lipopolysaccharide
Function / homologyother organism cell membrane / mast cell degranulation / chemotaxis / toxin activity / defense response to bacterium / innate immune response / extracellular region / membrane / Crabrolin
Function and homology information
Biological speciesVespa crabro (European hornet)
MethodSOLUTION NMR / na
AuthorsCantini, F. / Bouchemal, N. / Savarin, P. / Sette, M.
CitationJournal: J.Pept.Sci. / Year: 2020
Title: Effect of positive charges in the structural interaction of crabrolin isoforms with lipopolysaccharide.
Authors: Cantini, F. / Luzi, C. / Bouchemal, N. / Savarin, P. / Bozzi, A. / Sette, M.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 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 1.3Jun 19, 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: Crabrolin Plus, mutant of Crabrolin peptide


Theoretical massNumber of molelcules
Total (without water)1,5711
Polymers1,5711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1650 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Crabrolin Plus, mutant of Crabrolin peptide


Mass: 1571.048 Da / Num. of mol.: 1 / Mutation: L4K, T11R / Source method: obtained synthetically
Details: Peptides were purchased from Peptide Specialty Laboratories (GmbH, Germany), and purity was assayed by HPLC and mass spectrometry.
Source: (synth.) Vespa crabro (European hornet) / References: UniProt: P01518*PLUS

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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

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Sample preparation

DetailsType: micelle
Contents: 0.87 mM Crabrolin Plus, mutant of Crabrolin peptide, 14.6 uM Lipopolysaccharide, 95% H2O/5% D2O
Details: Peptides in the presence of lipopolysaccharides micelles
Label: sample1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.87 mMCrabrolin Plus, mutant of Crabrolin peptidenatural abundance1
14.6 uMLipopolysaccharidenatural abundance1
Sample conditionsDetails: 25 mM KPO4 pH 6.1 / Ionic strength: 125 mM / Label: Conditions / pH: 6.1 / Pressure: 760 mmHg / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: Cryoprobe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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