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- PDB-5ukz: NMR Solution structure of chemically synthesized antilisterial Pe... -

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Basic information

Entry
Database: PDB / ID: 5ukz
TitleNMR Solution structure of chemically synthesized antilisterial Pediocin PA-1 M31L analog.
ComponentsBacteriocin pediocin PA-1 M31L
KeywordsANTIMICROBIAL PROTEIN / Antilisterial / Pediocin PA-1 / Pediococcus acidilactici UL5 / Bacteriocin / Chemical synthesis
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Bacteriocin-type signal sequence / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Bacteriocin class IIa domain superfamily / Class II bacteriocin / Bacteriocin class IIa family signature.
Similarity search - Domain/homology
Bacteriocin pediocin PA-1
Similarity search - Component
Biological speciesPediococcus acidilactici (bacteria)
MethodSOLUTION NMR / na
AuthorsBedard, F. / Hammami, R. / Zirah, S. / Rebuffat, S. / Fliss, I. / Biron, E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)#2016-PR-191869 Canada
CitationJournal: Sci Rep / Year: 2018
Title: Synthesis, antimicrobial activity and conformational analysis of the class IIa bacteriocin pediocin PA-1 and analogs thereof.
Authors: Bedard, F. / Hammami, R. / Zirah, S. / Rebuffat, S. / Fliss, I. / Biron, E.
History
DepositionJan 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin pediocin PA-1 M31L


Theoretical massNumber of molelcules
Total (without water)4,6171
Polymers4,6171
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 / 40000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Bacteriocin pediocin PA-1 M31L / Pediocin ACH


Mass: 4617.172 Da / Num. of mol.: 1 / Fragment: UNP residues 19-62 / Mutation: M31L / Source method: obtained synthetically / Details: Pediocin PA-1 producer / Source: (synth.) Pediococcus acidilactici (bacteria) / References: UniProt: P29430
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 TOCSY
141anisotropic12D NOESY

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Sample preparation

DetailsType: solution
Contents: 3.33 mg/mL NA-1H Pediocin PA-1 M31L, trifluoroethanol/water
Details: 300 uL of 0.1% TFA water plus 300 uL of 98% TFE-d2.
Label: 1H_M31L / Solvent system: trifluoroethanol/water
SampleConc.: 3.33 mg/mL / Component: Pediocin PA-1 M31L / Isotopic labeling: NA-1H
Sample conditionsDetails: 0.1% TFA was required to prevet disulfide bond rearrangment while acquisitions. TOCSY and NOESY spectra were recorded with mixing times of 80 ms and 300 ms and 16 and 72 scans, respectively.
Ionic strength: 0 Not defined / Label: Conditions_1 / pH: 2.8 / PH err: 0.2 / Pressure: 1 atm / Temperature: 313 K / Temperature err: 0.1

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinchemical shift assignment
CS-ROSETTA3.7Shen, Vernon, Baker and Baxrefinement
CS-ROSETTA3.7Shen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
Details: For this entry, the authors only used chemical shift values without constraints. The authors used the CS-ROSETTA protocol which allows structure determination of proteins based on chemical ...Details: For this entry, the authors only used chemical shift values without constraints. The authors used the CS-ROSETTA protocol which allows structure determination of proteins based on chemical shift information alone.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40000 / Conformers submitted total number: 10

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