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- PDB-5z5r: Nukacin ISK-1 in inactive state -

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Basic information

Entry
Database: PDB / ID: 5z5r
TitleNukacin ISK-1 in inactive state
ComponentsLantibiotic nukacin
KeywordsANTIBIOTIC / lantibiotics
Function / homologyLantibiotic, type A, Lactobacillales-type / Type-A lantibiotic / cytolysis / defense response to bacterium / signaling receptor binding / extracellular region / Lantibiotic nukacin
Function and homology information
Biological speciesStaphylococcus warneri (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKohda, D. / Fujinami, D.
CitationJournal: Commun Biol / Year: 2018
Title: The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.
Authors: Fujinami, D. / Mahin, A.A. / Elsayed, K.M. / Islam, M.R. / Nagao, J.I. / Roy, U. / Momin, S. / Zendo, T. / Kohda, D. / Sonomoto, K.
History
DepositionJan 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lantibiotic nukacin


Theoretical massNumber of molelcules
Total (without water)2,9711
Polymers2,9711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2720 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Lantibiotic nukacin / Bacteriocin ISK-1


Mass: 2970.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus warneri (bacteria) / References: UniProt: Q9KWM4
Sequence detailsTHR39, SER41, AND SER48 ARE DEHYDRATED TO DBB39, DAL41 AND DAL48 BY POSTTRANSLATIONAL MODIFICATIONS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 1.1 mM nukacin ISK-1, 10 mM sodium phosphate, 90% H2O/10% D2O
Label: natural abundance / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMnukacin ISK-1natural abundance1
10 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 6.0 / Pressure: ambient Pa / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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