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- PDB-6sly: NMR solution structure of Helicobacter pylori TonB-CTD (residues ... -

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Basic information

Entry
Database: PDB / ID: 6sly
TitleNMR solution structure of Helicobacter pylori TonB-CTD (residues 179-285)
ComponentsProtein TonB
KeywordsMETAL TRANSPORT / TONB-DEPENDENT IRON UPTAKE / C-TERMINAL DOMAIN
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / energy transducer activity / siderophore transport / plasma membrane protein complex / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / membrane => GO:0016020 / plasma membrane
Similarity search - Function
TonB C-terminal domain profile. / Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal
Similarity search - Domain/homology
Protein TonB / Protein TonB
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCiragan, A. / Heikkinen, H.A. / Iwai, H.
Funding support Finland, 3items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Academy of Finland137995 Finland
Academy of Finland131413 Finland
Citation
Journal: Front Chem / Year: 2020
Title: NMR Structure and Dynamics of TonB Investigated by Scar-Less Segmental Isotopic Labeling Using a Salt-Inducible Split Intein.
Authors: Ciragan, A. / Backlund, S.M. / Mikula, K.M. / Beyer, H.M. / Samuli Ollila, O.H. / Iwai, H.
#1: Journal: Molecules / Year: 2021
Title: NMR Structure Determinations of Small Proteins Using only One Fractionally 20% 13 C- and Uniformly 100% 15 N-Labeled Sample.
Authors: Heikkinen, H.A. / Backlund, S.M. / Iwai, H.
History
DepositionAug 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.3Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
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 1.5Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TonB


Theoretical massNumber of molelcules
Total (without water)11,6141
Polymers11,6141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein TonB


Mass: 11614.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: EC544_07375 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A438WSV6, UniProt: O25899*PLUS

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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 HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA
171isotropic13D HN(CA)CO
181isotropic13D CBCA(CO)NH
191isotropic13D (H)CCH-COSY
1101isotropic13D H(CC)(CO)NH
1111isotropic13D (H)CC(CO)NH
1121isotropic13D 1H-15N NOESY
1131isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] TonB, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.5 mM / Component: TonB / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 mM / Label: sample_conditions_1 / pH: 6 / Pressure: 1 atm / Temperature: 303 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
NameVersionDeveloperClassification
CcpNMR2.4.1CCPNchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
TALOSNCornilescu, Delaglio and Baxchemical shift assignment
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
PSVS1.5Bhattacharya and Montelionedata analysis
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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