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- PDB-6qay: Structural investigation of the TasA anchoring protein TapA from ... -

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Basic information

Entry
Database: PDB / ID: 6qay
TitleStructural investigation of the TasA anchoring protein TapA from Bacillus subtilis
ComponentsTasA anchoring/assembly protein
KeywordsPROTEIN FIBRIL / TasA / TapA / anchoring / biofilm
Function / homologybacterial biofilm matrix / TasA anchoring/assembly protein / Signal peptide, camelysin / extracellular region / TasA anchoring/assembly protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHigman, V.A. / Schmieder, P. / Diehl, A. / Oschkinat, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: TapA acts as specific chaperone in TasA filament formation by strand complementation.
Authors: Roske, Y. / Lindemann, F. / Diehl, A. / Cremer, N. / Higman, V.A. / Schlegel, B. / Leidert, M. / Driller, K. / Turgay, K. / Schmieder, P. / Heinemann, U. / Oschkinat, H.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: TasA anchoring/assembly protein


Theoretical massNumber of molelcules
Total (without water)17,0101
Polymers17,0101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7040 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TasA anchoring/assembly protein / Biofilm assembly accessory protein TapA


Mass: 17010.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tapA, yqhD, yqxM, BSU24640 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 T7 Express / References: UniProt: P40949

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D 1H-15N NOESY
132isotropic12D 1H-13C HSQC
142isotropic13D 1H-13C NOESY
152isotropic23D CBCA(CO)NH
162isotropic23D HN(CA)CB
172isotropic23D C(CO)NH
1122isotropic23D H(CCO)NH
1112isotropic23D HBHA(CO)NH
1102isotropic23D (H)CCH-TOCSY
192isotropic23D HNCO
182isotropic23D HN(CO)CA

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] TasA anchoring/assembly protein, 50 mM sodium chloride, 20 mM potassium phosphate, 95% H2O/5% D2O15N95% H2O/5% D2O
solution20.54 mM [U-99% 13C; U-99% 15N] TasA anchoring/assembly protein, 50 mM sodium chloride, 20 mM potassium phosphate, 95% H2O/5% D2O13C15N95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTasA anchoring/assembly protein[U-99% 15N]1
50 mMsodium chloridenatural abundance1
20 mMpotassium phosphatenatural abundance1
0.54 mMTasA anchoring/assembly protein[U-99% 13C; U-99% 15N]2
50 mMsodium chloridenatural abundance2
20 mMpotassium phosphatenatural abundance2
Sample conditionsIonic strength: 76 mM / Label: standard / pH: 7 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: Standard ARIA water refinement protocol
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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