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- PDB-7ju9: Solution NMR structure of Prochlorosin 2.11 (Pcn2.11) produced by... -

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Basic information

Entry
Database: PDB / ID: 7ju9
TitleSolution NMR structure of Prochlorosin 2.11 (Pcn2.11) produced by Prochlorococcus MIT 9313
ComponentsProchlorosin 2.11
KeywordsUNKNOWN FUNCTION / lanthipeptide / cyclic peptide / posttranslational modification / RiPP
Function / homologyNif11 domain / Nif11-like leader peptide / Nif11 domain / Possible Vesiculovirus phosphoprotein
Function and homology information
Biological speciesProchlorococcus marinus str. MIT 9313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBobeica, S.C. / van der Donk, W.A. / Zhu, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM058822 United States
Citation
Journal: Chem Sci / Year: 2020
Title: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.
Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.
Authors: Li, B. / Sher, D. / Kelly, L. / Shi, Y. / Huang, K. / Knerr, P.J. / Joewono, I. / Rusch, D. / Chisholm, S.W. / van der Donk, W.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2017
Title: Evolutionary radiation of lanthipeptides in marine cyanobacteria.
Authors: Cubillos-Ruiz, A. / Berta-Thompson, J.W. / Becker, J.W. / van der Donk, W.A. / Chisholm, S.W.
#3: Journal: Biochemistry / Year: 2012
Title: Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria.
Authors: Tang, W. / van der Donk, W.A.
History
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionSep 9, 2020ID: 6VGP
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can ..._database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prochlorosin 2.11


Theoretical massNumber of molelcules
Total (without water)1,8311
Polymers1,8311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Prochlorosin 2.11 / Pcn2.11


Mass: 1831.042 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7V450*PLUS
Has ligand of interestY

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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 TOCSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
242isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM Prochlorosin 2.11, 90% H2O/10% D2OPcn2.1190% H2O/10% D2O
solution21 mM Prochlorosin 2.11, 100% D2OPcn2.11_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMProchlorosin 2.11natural abundance1
1 mMProchlorosin 2.11natural abundance2
Sample conditions

Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature err: 0.1

Conditions-IDLabelTemperature (K)
1Pcn2.11_details296 K
2Pcn2.11_D2O_details277 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKY2.51NMRFAMpeak picking
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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