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- PDB-7u37: Solution NMR structure of Vibrio cholerae ferrous iron transport ... -

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Basic information

Entry
Database: PDB / ID: 7u37
TitleSolution NMR structure of Vibrio cholerae ferrous iron transport protein C (FeoC)
ComponentsFerrous iron transport protein C
KeywordsCYTOSOLIC PROTEIN / FeoC / ferrous iron transport / Feo
Function / homologyTranscriptional regulator HTH-type, FeoC / FeoC like transcriptional regulator / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Ferrous iron transport protein C
Function and homology information
Biological speciesVibrio cholerae O1 (bacteria)
MethodSOLUTION NMR / na
AuthorsBrown, J.B. / Lee, M.A. / Smith, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133497 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM066706 United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2022
Title: The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain.
Authors: Brown, J.B. / Lee, M.A. / Smith, A.T.
History
DepositionFeb 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrous iron transport protein C


Theoretical massNumber of molelcules
Total (without water)8,5911
Polymers8,5911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160target function
RepresentativeModel #1target function

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Components

#1: Protein Ferrous iron transport protein C / Iron transporter FeoC


Mass: 8590.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria)
Gene: D6U24_00500, ERS013138_00486, ERS013165_00119, ERS013166_01719, ERS013173_02915, ERS013186_03225, ERS013193_04710, ERS013198_00924, ERS013199_01103, ERS013200_03657, ERS013202_01477, ERS013206_ ...Gene: D6U24_00500, ERS013138_00486, ERS013165_00119, ERS013166_01719, ERS013173_02915, ERS013186_03225, ERS013193_04710, ERS013198_00924, ERS013199_01103, ERS013200_03657, ERS013202_01477, ERS013206_03620, ERS013207_00898, EYB64_02470
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0B4M5

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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
121isotropic13D 1H-15N NOESY
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic14D HSQC-NOESY-HMQC
283isotropic14D HMQC-NOESY-HMQC
294isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium phosphate, 5 mM sodium chloride, 1 g/L [U-99% 15N] ammonium chloride, 300 uM [U-15N] Vibrio cholerae FeoC, 90% H2O/10% D2O15N90% H2O/10% D2O
solution250 mM sodium phosphate, 5 mM sodium chloride, 1 g/L [U-15N] ammonium chloride, 4 g/L [U-100% 13C] glucose, 300 uM [U-13C; U-15N] Vibrio cholerae FeoC, 90% H2O/10% D2O15N_13C90% H2O/10% D2O
solution350 mM sodium phosphate, 5 mM sodium chloride, 4 g/L [U-100% 13C] glucose, 300 uM [U-13C; U-15N] Vibrio cholerae FeoC, 100% D2O13C100% D2O
solution450 mM sodium phosphate, 5 mM sodium chloride, 300 uM [U-13C; U-15N] Vibrio cholerae FeoC, 100% D2OUL100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
5 mMsodium chloridenatural abundance1
1 g/Lammonium chloride[U-99% 15N]1
300 uMVibrio cholerae FeoC[U-15N]1
50 mMsodium phosphatenatural abundance2
5 mMsodium chloridenatural abundance2
1 g/Lammonium chloride[U-15N]2
4 g/Lglucose[U-100% 13C]2
300 uMVibrio cholerae FeoC[U-13C; U-15N]2
50 mMsodium phosphatenatural abundance3
5 mMsodium chloridenatural abundance3
4 g/Lglucose[U-100% 13C]3
300 uMVibrio cholerae FeoC[U-13C; U-15N]3
50 mMsodium phosphatenatural abundance4
5 mMsodium chloridenatural abundance4
300 uMVibrio cholerae FeoC[U-13C; U-15N]4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mMconditions_16 1 atm298 K
25 mMconditions_26 pD1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRFxJohnson, One Moon Scientificprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 160 / Conformers submitted total number: 20

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