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- PDB-5t56: [3]catenane from MccJ25 G12R/I13C/G21C lasso peptide -

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Basic information

Entry
Database: PDB / ID: 5t56
Title[3]catenane from MccJ25 G12R/I13C/G21C lasso peptide
Components(Microcin J25) x 2
KeywordsDE NOVO PROTEIN / Catenane / Lasso Peptide
Function / homologykilling of cells of another organism / defense response to bacterium / extracellular region / Microcin J25
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsLink, A.J. / Allen, C.D.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Self-Assembly of Catenanes from Lasso Peptides.
Authors: Allen, C.D. / Link, A.J.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcin J25
B: Microcin J25
C: Microcin J25
D: Microcin J25


Theoretical massNumber of molelcules
Total (without water)4,5614
Polymers4,5614
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein/peptide Microcin J25 / MccJ25


Mass: 1290.427 Da / Num. of mol.: 2 / Mutation: UNP residues 38-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcjA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2V7
#2: Protein/peptide Microcin J25 / MccJ25


Mass: 990.154 Da / Num. of mol.: 2 / Mutation: UNP residues 51-57
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcjA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X2V7
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 NOESY
121isotropic12D TOCSY

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Sample preparation

DetailsType: solution
Contents: 3.7 mg/mL [3]catenane from MccJ25 RCC lasso peptide, 95% H2O/5% D2O
Label: 1H_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 3.7 mg/mL / Component: [3]catenane from MccJ25 RCC lasso peptide / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / Pressure: ambient atm / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
GROMACS5.1.1Abraham, Hess, van der Spoel, Lindahlrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
MestReNova9.0.1Mestrelab Research S.L.data analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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