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- PDB-2keg: NMR structure of Plantaricin K in DPC-micelles -

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Basic information

Entry
Database: PDB / ID: 2keg
TitleNMR structure of Plantaricin K in DPC-micelles
ComponentsPlnK
KeywordsANTIMICROBIAL PROTEIN / Protein
Function / homologyPlnK
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRogne, P. / Haugen, M. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.
CitationJournal: Peptides / Year: 2009
Title: Three-dimensional structure of the two-peptide bacteriocin plantaricin JK.
Authors: Rogne, P. / Haugen, C. / Fimland, G. / Nissen-Meyer, J. / Kristiansen, P.E.
History
DepositionJan 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: 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: PlnK


Theoretical massNumber of molelcules
Total (without water)3,5101
Polymers3,5101
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 PlnK / Bacteriocin PlnK


Mass: 3509.958 Da / Num. of mol.: 1 / Fragment: bacteriocin peptide K / Source method: obtained synthetically / Source: (synth.) Lactobacillus plantarum (bacteria) / References: UniProt: P71460

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Part of two-peptide bacteriocin Plantaricin JK
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY
1412D DQF-COSY
1512D 1H-15N HSQC
1612D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM PlnK-1, 170 mM [U-99% 2H] DPC-2, 0.1 % TFA-3, 10 % D2O-4, 0.2 mM DSS-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPlnK-11
170 mMDPC-2[U-99% 2H]1
0.1 %TFA-31
10 %D2O-41
0.2 mMDSS-51
Sample conditionsIonic strength: 0 / pH: 2.5 / Pressure: ambient / Temperature: 312 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
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
MOLMOL2k2Koradi, Billeter and Wuthrichdata analysis
ACME2001.006.11.26Delaglio, Zhengrong and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 408 / NOE intraresidue total count: 99 / NOE long range total count: 0 / NOE medium range total count: 153 / NOE sequential total count: 156
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.12 Å

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