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- PDB-7cu6: lasso peptide C24 mutant - A11V2C -

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Basic information

Entry
Database: PDB / ID: 7cu6
Titlelasso peptide C24 mutant - A11V2C
Componentslasso peptide C24_A11V2C
KeywordsANTIBIOTIC / inhibitor / lasso peptide / natural product
Biological speciesStreptomyces sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMa, M. / Liu, X.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877002, 81673332, 81991525, 81573326 China
National Natural Science Foundation of China (NSFC)31570061 China
CitationJournal: Chem Sci / Year: 2021
Title: Rational generation of lasso peptides based on biosynthetic gene mutations and site-selective chemical modifications.
Authors: Liu, T. / Ma, X. / Yu, J. / Yang, W. / Wang, G. / Wang, Z. / Ge, Y. / Song, J. / Han, H. / Zhang, W. / Yang, D. / Liu, X. / Ma, M.
History
DepositionAug 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lasso peptide C24_A11V2C


Theoretical massNumber of molelcules
Total (without water)1,7511
Polymers1,7511
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide lasso peptide C24_A11V2C


Mass: 1751.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Streptomyces sp. (bacteria)

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 4.84 mM lasso peptide C24_A11V2C, 100 % Deuterated DMSO-d6, DMSO
Label: dmso_sample / Solvent system: DMSO
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4.84 mMlasso peptide C24_A11V2Cnatural abundance1
100 %DMSO-d6Deuterated1
Sample conditionsIonic strength: 0 mM / Label: condition_1 / pH: 7 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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