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- PDB-7k1q: Solution structure of lantibiotic from Paenibacillus sp. -

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Basic information

Entry
Database: PDB / ID: 7k1q
TitleSolution structure of lantibiotic from Paenibacillus sp.
ComponentsLantibiotic CMB001
KeywordsANTIMICROBIAL PROTEIN / lantipeptide / antimicrobial / stability / antibiotic resistance / MRSA
Function / homologyLantibiotic, Type A, Bacillales-type / Gallidermin / killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region / Lantibiotic
Function and homology information
Biological speciesPaenibacillus sp. (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKarczewski, J. / Diehl, C.
Citation
Journal: Front Microbiol / Year: 2020
Title: Isolation, Characterization and Structure Elucidation of a Novel Lantibiotic From Paenibacillus sp.
Authors: Karczewski, J. / Krasucki, S.P. / Asare-Okai, P.N. / Diehl, C. / Friedman, A. / Brown, C.M. / Maezato, Y. / Streatfield, S.J.
#1: Journal: Microbiology / Year: 2020
Title: Isolation, Characterization and Structure Elucidation of a Novel Lantibiotic From Paenibacillus sp.
Authors: Karczewski, J. / Krasucki, S.P. / Asare-Okai, P.N. / Diehl, C. / Friedman, P. / Brown, C.M. / Maezato, Y. / Streatfield, S.J.
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_database_related / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_related.details / _struct.title
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lantibiotic CMB001


Theoretical massNumber of molelcules
Total (without water)3,4561
Polymers3,4561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Lantibiotic CMB001


Mass: 3456.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paenibacillus sp. (bacteria) / References: UniProt: A0A1E3KYX3*PLUS
Has ligand of interestY
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
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H COSY
141isotropic12D 1H-1H NOESY
151isotropic12D 1H-1H NOESY
161isotropic12D 1H-1H TOCSY
171isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution / Contents: 5.7 mM CMB001, DMSO / Details: 5.7 mM CMB001 in DMSO-d6 / Label: CMB001 / Solvent system: DMSO
SampleConc.: 5.7 mM / Component: CMB001 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 M / Label: CMB001 / pH: 0 Not defined / Pressure: 1 bar / Temperature: 298 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
GROMACSLindahl, Abraham, Hess, van der Spoelrefinement
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
GROMACSLindahl, Abraham, Hess, van der Spoelstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 60 / Conformers submitted total number: 15

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