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- PDB-6vhj: Solution NMR of Prochlorosin 1.1 produced by Prochlorococcus MIT 9313 -

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Basic information

Entry
Database: PDB / ID: 6vhj
TitleSolution NMR of Prochlorosin 1.1 produced by Prochlorococcus MIT 9313
ComponentsProchlorosin 1.1
KeywordsUNKNOWN FUNCTION / lanthipeptide / cyclic peptide / posttranslational modification / RiPP
Function / homologyNif11 domain / Nif11-like leader peptide / Nif11 domain / extracellular region / Lantipeptide prochlorosin 1.1
Function and homology information
Biological speciesProchlorococcus marinus str. MIT 9313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBobeica, S.C. / van der Donk, W.A. / Tang, W.
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: Chem Sci / Year: 2020
Title: Correction: 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.
#2: 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.
#3: Journal: Nat.Chem.Biol. / Year: 2013
Title: The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.
Authors: Tang, W. / van der Donk, W.A.
#4: 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.
#5: 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.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 9, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nmr_ensemble ...atom_site / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_struct_assembly / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_ensemble.conformers_calculated_total_number / _pdbx_nmr_refine.software_ordinal / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_conn.pdbx_dist_value
Description: Chirality error
Details: Residue DBB 12 should have been (S) configuration at CB. An additional improper angle was added to the XPLOR patch command to ensure DL-(methyl)lanthionine linkages maintain (S) configuration at CB.
Provider: author / Type: Coordinate replacement
Revision 2.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Revision 2.2Jun 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 3.0Jul 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 / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prochlorosin 1.1


Theoretical massNumber of molelcules
Total (without water)1,7891
Polymers1,7891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with acceptable covalent geometry
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Prochlorosin 1.1


Mass: 1789.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria)
Details (production host): Peptide is purified N-terminally His6-tagged from co-expression with ProcM
Production host: Escherichia coli (E. coli) / References: UniProt: Q7V8T1*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-1H TOCSY
121isotropic12D 1H-1H NOESY
232isotropic12D 1H-1H TOCSY
242isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM Prochlorosin 1.1, 90% H2O/10% D2OPcn1.190% H2O/10% D2O
solution22 mM Prochlorosin 1.1, 100% D2OPcn1.1_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMProchlorosin 1.1natural abundance1
2 mMProchlorosin 1.1natural abundance2
Sample conditions

Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature: 296 K / Temperature err: 0.1

Conditions-IDLabel
1Pcn1.1_H2O
2Pcn1.1_D2O

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 20

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