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- PDB-5lw8: NMR solution structure of Helicobacter pylori TonB-CTD (residues ... -

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Basic information

Entry
Database: PDB / ID: 5lw8
TitleNMR solution structure of Helicobacter pylori TonB-CTD (residues 194-285)
ComponentsProtein TonB
KeywordsMETAL TRANSPORT / TonB-dependent iron uptake / C-terminal domain / proline rich domain
Function / homology
Function and homology information


energy transducer activity / siderophore transport / plasma membrane protein complex / transmembrane transport / protein transport / outer membrane-bounded periplasmic space
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
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsCiragan, A. / Aranko, A.S. / Tascon, I. / Iwai, H.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Salt-inducible Protein Splicing in cis and trans by Inteins from Extremely Halophilic Archaea as a Novel Protein-Engineering Tool.
Authors: Ciragan, A. / Aranko, A.S. / Tascon, I. / Iwai, H.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Structure summary
Revision 1.2Nov 30, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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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)10,1521
Polymers10,1521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #11lowest energy

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Components

#1: Protein Protein TonB


Mass: 10151.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Gene: tonB, HP_1341 / Production host: Escherichia coli (E. coli) / References: UniProt: O25899

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic12D 1H-15N HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
191isotropic13D 1H-15N TOCSY
181isotropic13D CBCA(CO)NH
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D (H)CCH-COSY
1101isotropic12D 1H-13C HSQC
1131isotropic13D H(CCO)NH
1121isotropic13D HNCA
1141isotropic13D HBHA(CO)NH
NMR detailsText: 3D 1H-15N NOESY and 3D 1H-13C NOESY spectra were recorded with a mixing time of 90 ms.

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] TonB CTD, 90% H2O/10% D2O
Details: 20 mM sodium phosphate buffer, pH 6.0 / Label: 15N13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: TonB CTD / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.02 mM / Label: 0 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.1CCPNchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Amber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
PSVS1.5Bhattacharya and Montelionedata analysis
TALOSchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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