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- PDB-2d1u: Solution structure of the periplasmic signaling domain of FecA fr... -

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Basic information

Entry
Database: PDB / ID: 2d1u
TitleSolution structure of the periplasmic signaling domain of FecA from Escherichia coli
ComponentsIron(III) dicitrate transport protein fecA
KeywordsMETAL TRANSPORT / FecA / Surface signaling / Iron-uptake
Function / homology
Function and homology information


response to iron ion starvation / siderophore-iron transmembrane transporter activity / siderophore-dependent iron import into cell / signal transduction involved in regulation of gene expression / transmembrane transporter complex / cell outer membrane / signaling receptor activity / iron ion transport / intracellular iron ion homeostasis / regulation of DNA-templated transcription / membrane
Similarity search - Function
: / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site ...: / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor (TBDR) proteins signature 1. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / 3-Layer(bab) Sandwich / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Alpha Beta
Similarity search - Domain/homology
Fe(3+) dicitrate transport protein FecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsGarcia-Herrero, A. / Vogel, H.J.
CitationJournal: Mol.Microbiol. / Year: 2005
Title: Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli
Authors: Garcia-Herrero, A. / Vogel, H.J.
History
DepositionSep 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: pdbx_nmr_software / pdbx_nmr_spectrometer ...pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct / struct_ref_seq_dif
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model ..._pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct.title / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron(III) dicitrate transport protein fecA


Theoretical massNumber of molelcules
Total (without water)11,1521
Polymers11,1521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Iron(III) dicitrate transport protein fecA


Mass: 11152.094 Da / Num. of mol.: 1 / Fragment: periplasmic signaling domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fecA / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13036

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated ROESY
1223D 13C-separated NOESY
1332D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM NTFecA U-15N; 50mM phosphate buffer; 90% H20, 10% D2O90% H20, 10% D2O
21mM NTFecA U-15N, 13C; 50mM phosphate buffer pH6; 90% H20, 10% D2O90% H20, 10% D2O
31mM NTFecA U-15N; 50mM phosphate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM sodium phosphate / pH: 6 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Peter Guntertstructure solution
CYANA2Peter Guntertrefinement
NMRView5.0.4Bruce johnsondata analysis
NMRPipe2.3 rev 2004.194.17.02Frank delaglioprocessing
XwinNMR3Brukercollection
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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