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- PDB-8qrx: Solution NMR structure of the peptidyl carrier domain TomAPCP fro... -

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Basic information

Entry
Database: PDB / ID: 8qrx
TitleSolution NMR structure of the peptidyl carrier domain TomAPCP from the Tomaymycin non-ribosomal peptide synthetase in its substrate-loaded state
ComponentsTomAPCP substrate-loaded from the Tomaymycin non-ribosomal peptide synthetase
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / NRPS / Tomaymycin / Peptidyl carrier protein / PCP / phosphopantetheine / Donor / loaded / substrate-loaded
Biological speciesStreptomyces regensis (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics / molecular dynamics
AuthorsKaranth, M.N. / Kirkpatrick, J.P. / Carlomagno, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CA294/16-1 Germany
CitationJournal: Sci Adv / Year: 2024
Title: The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain.
Authors: Karanth, M.N. / Kirkpatrick, J.P. / Krausze, J. / Schmelz, S. / Scrima, A. / Carlomagno, T.
History
DepositionOct 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TomAPCP substrate-loaded from the Tomaymycin non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)10,4831
Polymers10,4831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein TomAPCP substrate-loaded from the Tomaymycin non-ribosomal peptide synthetase


Mass: 10483.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the ...Details: First four residues (GPMA) in the protein are from cloning artifacts. Therefore, the appropriate residue numbering has the first residue (G) designated as residue-number '-3', so that the fifth residue has residue-number '1'. A special modified residue SPA is designated for the serine residue covalently linked to a 4'-phosphopantetheine-anthranilate prosthetic group.
Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli (E. coli)
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-15N HSQC
123isotropic22D 1H-13C HSQC
132isotropic22D 1H-13C HSQC
141isotropic13D 1H-15N NOESY
152isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1350 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution3100 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2O13C15N_sample_290% H2O/10% D2O
solution2500 uM [U-13C; U-15N] TomAPCP substrate-loaded, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v sodium azide, 100 v/v [U-2H] D2O, 100% D2O13C15N_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMTomAPCP substrate-loaded[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.02 w/vsodium azidenatural abundance1
10 v/vD2O[U-2H]1
100 uMTomAPCP substrate-loaded[U-13C; U-15N]3
50 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
0.02 w/vsodium azidenatural abundance3
10 v/vD2O[U-2H]3
500 uMTomAPCP substrate-loaded[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.02 % w/vsodium azidenatural abundance2
100 v/vD2O[U-2H]2
Sample conditionsIonic strength: 265 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
NMRPipe10.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4CCPNpeak picking
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing7
torsion angle dynamics8
molecular dynamics9
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: 10

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