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- PDB-2rlw: Three-Dimensional Structure of the two Peptides that Constitute t... -

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Basic information

Entry
Database: PDB / ID: 2rlw
TitleThree-Dimensional Structure of the two Peptides that Constitute the Two-Peptide Bacteriocin Plantaracin EF
ComponentsPlnF
KeywordsTOXIN / peptide plnF
Function / homologyBacteriocin
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsFimland, N. / Rogne, P. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin plantaricin EF
Authors: Fimland, N. / Rogne, P. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.E.
History
DepositionAug 27, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PlnF


Theoretical massNumber of molelcules
Total (without water)3,7091
Polymers3,7091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PlnF / Bacteriocin peptide PlnF


Mass: 3709.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: C11 / Gene: plnF / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: P71469

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1413D 1H-15N TOCSY
1513D 1H-15N NOESY
1613D HNHA

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Sample preparation

DetailsContents: 0.2 mM DSS, 0.1 % TFA, 200 mM [U-2H] DPC, 1 mM [U-95% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMDSS1
0.1 %TFA1
200 mMDPC[U-2H]1
1 mMentity[U-95% 15N]1
Sample conditionsIonic strength: 0 / pH: 2.5 / Pressure: ambient / Temperature: 303 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
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSDelagliotorsion angle determination
SparkyGoddardchemical shift assignment
TopSpinBrukerprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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