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- PDB-6rfm: Bordetella pertussis adenylate cyclase toxin transmembrane segmen... -

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Basic information

Entry
Database: PDB / ID: 6rfm
TitleBordetella pertussis adenylate cyclase toxin transmembrane segment 411-490 in DPC micelles
ComponentsBifunctional hemolysin/adenylate cyclase
KeywordsTOXIN / adenylate cyclase / Bordetella pertussis / membrane protein / calcium binding
Function / homology
Function and homology information


calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration ...calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site ...RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Bifunctional hemolysin/adenylate cyclase / Bifunctional hemolysin/adenylate cyclase
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMasin, J. / Bumba, L. / Veverka, V.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2020
Title: Negative charge of the AC-to-Hly linking segment modulates calcium-dependent membrane activities of Bordetella adenylate cyclase toxin.
Authors: Sukova, A. / Bumba, L. / Srb, P. / Veverka, V. / Stanek, O. / Holubova, J. / Chmelik, J. / Fiser, R. / Sebo, P. / Masin, J.
History
DepositionApr 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: citation / database_2 ...citation / database_2 / pdbx_database_status / struct_ref
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional hemolysin/adenylate cyclase


Theoretical massNumber of molelcules
Total (without water)8,2261
Polymers8,2261
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 area7980 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Bifunctional hemolysin/adenylate cyclase / AC-HLY / ACT / Cyclolysin


Mass: 8226.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cya, cyaA, BN118_0468 / Production host: Escherichia coli (E. coli)
References: UniProt: J7QLC0, UniProt: P0DKX7*PLUS, adenylate cyclase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D (H)CCH-TOCSY
151isotropic13D 1H-13C NOESY
161isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: micelle
Contents: 450 uM [U-13C; U-15N] Cya411-490, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 100 mM [U-2H] DPC, 90% H2O/10% D2O
Label: s1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMCya411-490[U-13C; U-15N]1
25 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
100 mMDPC[U-2H]1
Sample conditionsIonic strength: 125 mM / Label: c1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
YASARAYASARArefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 50

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