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- PDB-6gif: AapA1 V26A toxin from helicobacter pylori 26695 -

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Basic information

Entry
Database: PDB / ID: 6gif
TitleAapA1 V26A toxin from helicobacter pylori 26695
ComponentsAapA1
KeywordsTOXIN / AapA1 V26A toxin from helicobacter pylori 26695
Function / homologyUncharacterized protein
Function and homology information
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKorkut, D.N. / Salgado, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Structural insights into the AapA1 toxin of Helicobacter pylori.
Authors: Korkut, D.N. / Alves, I.D. / Vogel, A. / Chabas, S. / Sharma, C.M. / Martinez, D. / Loquet, A. / Salgado, G.F. / Darfeuille, F.
History
DepositionMay 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Sep 11, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.3Dec 4, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.4Jun 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 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AapA1


Theoretical massNumber of molelcules
Total (without water)3,4431
Polymers3,4431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3210 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide AapA1


Mass: 3443.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori SS1 (bacteria) / References: UniProt: A0A1Y3E6H1

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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 NOESY
121isotropic22D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM no labeling AapA1 V26A, 10 mM deuterated acetic acid, 10 mM deuterated DTT, 40 % deuterated TFE, trifluoroethanol/water
Label: AapA1 V26A buffer A / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAapA1 V26Ano labeling1
10 mMacetic aciddeuterated1
10 mMDTTdeuterated1
40 %TFEdeuterated1
Sample conditionsIonic strength: 10 mM / Label: buffer A / pH: 4.7 Not defined / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 2000 / Conformers submitted total number: 10

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