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- PDB-2k9k: Molecular characterization of the tonb2 protein from vibrio angui... -

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Basic information

Entry
Database: PDB / ID: 2k9k
TitleMolecular characterization of the tonb2 protein from vibrio anguillarum
ComponentsTonB2
KeywordsMETAL TRANSPORT / TonB2-CTD
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
Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / : / 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 speciesListonella anguillarum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLopez, C.S. / Peacock, R.S. / Crosa, J.H. / Vogel, H.J.
CitationJournal: Biochem.J. / Year: 2009
Title: Molecular characterization of the TonB2 protein from the fish pathogen Vibrio anguillarum.
Authors: Lopez, C.S. / Peacock, R.S. / Crosa, J.H. / Vogel, H.J.
History
DepositionOct 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: TonB2


Theoretical massNumber of molelcules
Total (without water)11,8921
Polymers11,8921
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 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein TonB2


Mass: 11891.554 Da / Num. of mol.: 1 / Fragment: TonB2 C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listonella anguillarum (bacteria) / Gene: tonB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SDB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D HN(CO)CA
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] TonB2-CTD, 90 % D2O, 1 mM DSS, 10 mM H2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTonB2-CTD[U-100% 13C; U-100% 15N]1
90 %D2O1
1 mMDSS1
10 mMH2O1
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA102Guntert, Mumenthaler and Wuthrichstructure solution
CYANA102Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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