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- PDB-6xti: NMR solution structure of class IV lasso peptide felipeptin A2 fr... -

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Basic information

Entry
Database: PDB / ID: 6xti
TitleNMR solution structure of class IV lasso peptide felipeptin A2 from Amycolatopsis sp. YIM10
ComponentsFelipeptin A2
KeywordsUNKNOWN FUNCTION / lasso peptide / antibacterial / class IV
Function / homologyUncharacterized protein
Function and homology information
Biological speciesAmycolatopsis sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMadland, E. / Aachmann, F.L. / Guerrero-Garzon, J.F. / Zotchev, S.B. / Courtade, G.
Funding support Austria, Denmark, 2items
OrganizationGrant numberCountry
Other governmentUniversity of Vienna Austria
Novo Nordisk FoundationNNF18OC0032242 Denmark
CitationJournal: Iscience / Year: 2020
Title: Class IV Lasso Peptides Synergistically Induce Proliferation of Cancer Cells and Sensitize Them to Doxorubicin.
Authors: Guerrero-Garzon, J.F. / Madland, E. / Zehl, M. / Singh, M. / Rezaei, S. / Aachmann, F.L. / Courtade, G. / Urban, E. / Ruckert, C. / Busche, T. / Kalinowski, J. / Cao, Y.R. / Jiang, Y. / ...Authors: Guerrero-Garzon, J.F. / Madland, E. / Zehl, M. / Singh, M. / Rezaei, S. / Aachmann, F.L. / Courtade, G. / Urban, E. / Ruckert, C. / Busche, T. / Kalinowski, J. / Cao, Y.R. / Jiang, Y. / Jiang, C.L. / Selivanova, G. / Zotchev, S.B.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Felipeptin A2


Theoretical massNumber of molelcules
Total (without water)1,8671
Polymers1,8671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide Felipeptin A2


Mass: 1867.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis sp. (bacteria) / Variant: YIM10 / Production host: Streptomyces coelicolor (bacteria) / Variant (production host): M1154 / References: UniProt: A0A5P9PSL4*PLUS
Has ligand of interestN

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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 DQF-COSY
141isotropic12D 1H-1H TOCSY
151isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 0.5 mM Felipeptin A2, DMSO / Label: sample_1 / Solvent system: DMSO
SampleConc.: 0.5 mM / Component: Felipeptin A2 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0.5 mM / Label: conditions_1 / pH: 7 Not defined / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
Refinement
MethodSoftware ordinal
simulated annealing3
simulated annealing4
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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