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- PDB-2kto: Spatial structure of Lch-beta peptide from two-component lantibio... -

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Basic information

Entry
Database: PDB / ID: 2kto
TitleSpatial structure of Lch-beta peptide from two-component lantibiotic Lichenicidin VK21
ComponentsLCHB
KeywordsANTIBIOTIC / LICHENICIDIN VK21 / LANTIBIOTICS / LCHB / LANTHIONINE / THIOESTER / TWO-COMPONENT LANTIBIOTIC SYSTEM
Function / homologyType 2 lantibiotic, SP_1948 family / Two-component Enterococcus faecalis cytolysin (EFC) / cytolysis / defense response to Gram-positive bacterium / signaling receptor binding / extracellular space / BETA LICHENICIDIN PREPEPTIDE / Lantibiotic lichenicidin VK21 A2
Function and homology information
Biological speciesBACILLUS LICHENIFORMIS (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMineev, K.S. / Shenkarev, Z.O. / Ovchinnikova, T.V. / Arseniev, A.S.
CitationJournal: Biochemistry / Year: 2010
Title: Isolation, Structure Elucidation, and Synergistic Antibacterial Activity of a Novel Two-Component Lantibiotic Lichenicidin from Bacillus Licheniformis Vk21.
Authors: Shenkarev, Z.O. / Finkina, E.I. / Nurmukhamedova, E.K. / Balandin, S.V. / Mineev, K.S. / Nadezhdin, K.D. / Yakimenko, Z.A. / Tagaev, A.A. / Temirov, Y.V. / Arseniev, A.S. / Ovchinnikova, T.V.
History
DepositionFeb 5, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 20, 2011Group: Structure summary
Revision 1.4Aug 10, 2011Group: Structure summary
Revision 1.5Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: LCHB


Theoretical massNumber of molelcules
Total (without water)3,0321
Polymers3,0321
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1

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Components

#1: Protein/peptide LCHB / Lantibiotic lichenicidin VK21 A2 / LchA2


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 3031.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AMINO ACIDS AND THE FORMATION OF ...Details: LICHENICIDIN VK21 IS A TETRACYCLIC PEPTIDE. POST TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES THE ENZYMIC CONVERSION OF THR, AND SER INTO DEHYDRATED AMINO ACIDS AND THE FORMATION OF THIOETHER BONDS WITH CYSTEINE. THIOETHER BONDS WITH CYSTEINE RESULT IN FOUR RINGS. THIS IS FOLLOWED BY MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED PRECURSOR.
Source: (natural) BACILLUS LICHENIFORMIS (bacteria) / Strain: VK21 / References: UniProt: P86476, BETA LICHENICIDIN PREPEPTIDE
Compound detailsLICHENICIDIN VK21 A2 IS A LANTIBIOTIC. THE LANTIBIOTICS ARE ARE CHARACTERIZED BY THIOESTER AMINO ...LICHENICIDIN VK21 A2 IS A LANTIBIOTIC. THE LANTIBIOTICS ARE ARE CHARACTERIZED BY THIOESTER AMINO ACIDS LANTHIONINE AND/OR METHYLLANTHIONINE. HERE, LICHENICIDIN VK21 IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
2212D 1H-1H NOESY
3312D 1H-1H TOCSY
4412D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5 MM LCHB-1, 500 MG [U-100% 2H] METHANOL-2, METHANOL
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLchB-11
500 mg/mLmethanol-2[U-100% 2H]1
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: AMBIENT / Temperature: 300 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 software
NameDeveloperClassification
CYANA 2.1GUNTERT, MUMENTHALERrefinement
CARA 1.5.3structure solution
TOPSPIN 2.1structure solution
CYANA 2.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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