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- PDB-6pqg: Solution structure of OlvA(BC) -

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Basic information

Entry
Database: PDB / ID: 6pqg
TitleSolution structure of OlvA(BC)
ComponentsOlvA(BC)
KeywordsRIBOSOMAL PROTEIN / Lanthipeptide / RiPPs
Biological speciesStreptomyces olivaceus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAcedo, J.Z. / van der Donk, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R37 GM058822 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: O-Methyltransferase-Mediated Incorporation of a beta-Amino Acid in Lanthipeptides.
Authors: Acedo, J.Z. / Bothwell, I.R. / An, L. / Trouth, A. / Frazier, C. / van der Donk, W.A.
History
DepositionJul 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 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: OlvA(BC)


Theoretical massNumber of molelcules
Total (without water)1,6171
Polymers1,6171
Non-polymers00
Water0
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide OlvA(BC)


Mass: 1616.841 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces olivaceus (bacteria) / Production host: Escherichia coli (E. coli)
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-1H TOCSY
121isotropic12D 1H-1H NOESY
132isotropic12D 1H-1H TOCSY
142isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.5 mM NA OlvA(BC), 30 mM NA sodium phosphate, 0.001 % NA DSS, 90% H2O/10% D2OOlvA(BC)90% H2O/10% D2O
solution22.5 mM NA OlvA(BC), 30 mM NA sodium phosphate, 0.001 % NA DSS, 100% D2OOlvA(BC)_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMOlvA(BC)NA1
30 mMsodium phosphateNA1
0.001 %DSSNA1
2.5 mMOlvA(BC)NA2
30 mMsodium phosphateNA2
0.001 %DSSNA2
Sample conditionsIonic strength: 30 mM / Label: conditions_1 / pH: 5.8 / Pressure: 760 mmHg / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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