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- PDB-1xx3: Solution Structure of Escherichia coli TonB-CTD -

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Basic information

Entry
Database: PDB / ID: 1xx3
TitleSolution Structure of Escherichia coli TonB-CTD
ComponentsTonB protein
KeywordsTRANSPORT PROTEIN / TonB-CTD / C-terminal domain
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / siderophore transport / cell envelope / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / cell outer membrane ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / siderophore transport / cell envelope / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein domain specific binding / membrane / plasma membrane
Similarity search - Function
TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / : / Gram-negative bacterial TonB protein / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal ...TolA/TonB C-terminal domain / TonB / : / TonB polyproline region / : / Gram-negative bacterial TonB protein / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / This structure was refined using standard Aria2.0 protocols (distance geometry,simulated annealing, torsion angle dynamics, water refinement)
AuthorsPeacock, R.S. / Weljie, A.M. / Howard, S.P. / Price, F.D. / Vogel, H.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The solution structure of the C-terminal domain of TonB and interaction studies with TonB box peptides
Authors: Peacock, R.S. / Weljie, A.M. / Howard, S.P. / Price, F.D. / Vogel, H.J.
History
DepositionNov 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB protein


Theoretical massNumber of molelcules
Total (without water)16,0361
Polymers16,0361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TonB protein


Mass: 16036.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB, exbA / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02929

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 15N-separated NOESY
1423D 13C-separated NOESY
1533D 15N-separated NOESY
1633D 13C-separated NOESY
NMR detailsText: This structure was determined using standard triple-resonance NMR spectroscopy techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM TonB-CTD U-15N,13C; 50 mM Sodium Phosphate buffer; 100 mM NaCl; 600 uM Sodium Azide, 90% H2O 10% D2O90% H2O/10% D2O
21.0 mM TonB-CTD U-15N; 50 mM Sodium Phosphate buffer; 100 mM NaCl ; 600 uM Sodium Azide; pH 7.0, 90% H2O 10% D2O90% H2O/10% D2O
31.0 mM TonB-CTD U-15N; 50 mM Sodium Phosphate buffer; 100 mM NaCl; 600 uM Sodium Azide; pH 7.0, 100% D2O100% D2O
Sample conditionsIonic strength: 100 mM Sodium Chloride, 50 mM Sodium Phosphate
pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.0, 3.5Brukercollection
NMRPipe2.3 Rev 2004.194.17.02Frank Delaglioprocessing
NMRView5.0.4Bruce Johnsondata analysis
ARIA2Michael Nilges et al.data analysis
CNS1.1Axel Brunger et al.refinement
RefinementMethod: This structure was refined using standard Aria2.0 protocols (distance geometry,simulated annealing, torsion angle dynamics, water refinement)
Software ordinal: 1
Details: The structures are based on a total of 2711 restraints, 2544 of which are NOE-derived, 21 of which are hydrogen bond restraints, and 146 of which are dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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