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- PDB-8qfa: Solution structure of the extreme C-terminus of the Bordetella pe... -

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Basic information

Entry
Database: PDB / ID: 8qfa
TitleSolution structure of the extreme C-terminus of the Bordetella pertussis filamentous hemagglutinin prodomain
ComponentsFHA protein
KeywordsCELL ADHESION / FHA / FhaB / extreme C terminus / Bordetella
Function / homology
Function and homology information


Filamentous haemagglutinin repeat / Haemagglutinin repeat / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / ESPR domain / Extended Signal Peptide of Type V secretion system / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesBordetella pertussis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsJurnecka, D. / Chmelik, J. / Bumba, L.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation22-23578S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2023053 Czech Republic
CitationJournal: To Be Published
Title: Solution structure of the extreme C-terminus of the Bordetella pertussis filamentous hemagglutinin prodomain
Authors: Jurnecka, D. / Chmelik, J. / Bumba, L.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FHA protein


Theoretical massNumber of molelcules
Total (without water)12,0161
Polymers12,0161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein FHA protein


Mass: 12015.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: CIP 81.32 / Gene: fhaB2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 {lambda}DE3 / References: UniProt: Q8VV99

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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
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D HNCA
181isotropic13D HN(CO)CA
191isotropic13D (H)CC(CO)NH
1101isotropic13D H(CCO)NH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-TOCSY aromatic
1131isotropic12D (HB)CB(CGCD)HD
1141isotropic12D (HB)CB(CGCDCE)HE
1151isotropic13D 1H-15N NOESY
1161isotropic13D 1H-13C NOESY aliphatic
1171isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] FHA-ECT, 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM disodium phosphate, 1.8 mM monopotassium phosphate, 0.1 % sodium azide, 90 % v/v H2O, 10 % v/v [U-2H] D2O, 90% H2O/10% D2O
Details: volume=550 ul / Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMFHA-ECT[U-13C; U-15N]1
137 mMsodium chloridenatural abundance1
2.7 mMpotassium chloridenatural abundance1
10 mMdisodium phosphatenatural abundance1
1.8 mMmonopotassium phosphatenatural abundance1
0.1 %sodium azidenatural abundance1
90 % v/vH2Onatural abundance1
10 % v/vD2O[U-2H]1
Sample conditionsIonic strength: 171.5 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY1.2Lee, Tonelli, Markleychemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RECOORDNederveen, Doreleijers, Vranken, Miller, Spronk, Nabuurs, Guntert, Livny, Markley, Nilges, Ulrich, Kaptein, Bonvinrefinement
NMRFAM-SPARKY1.2Lee, Tonelli, Markleypeak picking
TopSpin3.5.7Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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