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- PDB-8rd6: the C-terminal domain of TonB protein from Salmonella enterica. -

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Basic information

Entry
Database: PDB / ID: 8rd6
Titlethe C-terminal domain of TonB protein from Salmonella enterica.
ComponentsProtein TonB
KeywordsTRANSPORT PROTEIN / PROTEIN / TonB
Function / homology
Function and homology information


energy transducer activity / bacteriocin transport / siderophore transport / plasma membrane protein complex / transmembrane transport / protein transport / outer membrane-bounded periplasmic space
Similarity search - Function
TonB polyproline region / 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
Biological speciesSalmonella enterica (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIwai, H. / Ciragan, A. / Oeemig, J.S.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland118385 Finland
Academy of Finland131413 Finland
Academy of Finland137995 Finland
Academy of Finland277335 Finland
CitationJournal: Sci Data / Year: 2024
Title: The 100-protein NMR spectra dataset: A resource for biomolecular NMR data analysis.
Authors: Klukowski, P. / Damberger, F.F. / Allain, F.H. / Iwai, H. / Kadavath, H. / Ramelot, T.A. / Montelione, G.T. / Riek, R. / Guntert, P.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein TonB


Theoretical massNumber of molelcules
Total (without water)10,0551
Polymers10,0551
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein TonB


Mass: 10054.522 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: tonB, STM1737 / Plasmid: pRSF / Production host: Escherichia coli B (bacteria) / References: UniProt: P25945

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1NOESY
121isotropic3NOESY

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Sample preparation

DetailsType: solution
Contents: 1.1 mM [U-100% 13C; U-100% 15N] TonB-CTD(154-242), 90% H2O/10% D2O
Details: 1.1mM TonB in 20mM Kpi pH 6.0 / Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.1 mM / Component: TonB-CTD(154-242) / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 mM / Label: DL_2015 / pH: 6 / Pressure: AMBIENT atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker AVANCE IIIBrukerAVANCE III9503

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guentertstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CcpNmr Analysis2CCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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