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- PDB-8qsx: Solution NMR structure of the novel adaptor domain TomBN91 from t... -

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Basic information

Entry
Database: PDB / ID: 8qsx
TitleSolution NMR structure of the novel adaptor domain TomBN91 from the Tomaymycin non-ribosomal peptide synthetase
ComponentsTomBN91
KeywordsBIOSYNTHETIC PROTEIN / Non-ribosomal peptide synthetase / NRPS / Tomaymycin / novel protein / Adaptor protein
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 11, 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TomBN91


Theoretical massNumber of molelcules
Total (without water)9,9851
Polymers9,9851
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 #3closest to the average

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Components

#1: Protein TomBN91


Mass: 9985.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First four residues (GPML) 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 (GPML) 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'.
Source: (gene. exp.) Streptomyces regensis (bacteria) / Variant: FH6421 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D HN(COCA)CB
171isotropic13D HN(CO)CA
181isotropic13D (H)CCH-TOCSY
191isotropic13D TOCSY-HSQC
1101isotropic13D HBHA(CO)NH
1112isotropic13D 1H-15N NOESY
1123isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM [U-13C; U-15N] Non-ribosomal protein TomBN91, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 10 % v/v [U-2H] D2O, 90% H2O/10% D2OMain sample used for assignment13C15N_sample90% H2O/10% D2O
solution3800 uM [U-13C; U-15N] TomBN91, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 10 % v/v [U-2H] D2O, 90% H2O/10% D2OSample used for collection of distance restraints.13C15N_sample_290% H2O/10% D2O
solution2300 uM [U-15N] TomBN91, 50 mM sodium phosphate, 150 mM sodium chloride, 1 mM TCEP, 0.02 % w/v sodium azide, 10 v/v [U-2H] D2O, 90% H2O/10% D2OSample used for collection of distance restraints.15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMNon-ribosomal protein TomBN91[U-13C; U-15N]1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
0.02 % w/vsodium azidenatural abundance1
10 % v/vD2O[U-2H]1
800 uMTomBN91[U-13C; U-15N]3
50 mMsodium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
1 mMTCEPnatural abundance3
0.02 % w/vsodium azidenatural abundance3
10 % v/vD2O[U-2H]3
300 uMTomBN91[U-15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
1 mMTCEPnatural abundance2
0.02 % w/vsodium azidenatural abundance2
10 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 III HDBrukerAVANCE III HD6001
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Refinement
MethodSoftware ordinal
simulated annealing6
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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