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- PDB-1zzv: Solution NMR Structure of the Periplasmic Signaling Domain of the... -

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Basic information

Entry
Database: PDB / ID: 1zzv
TitleSolution NMR Structure of the Periplasmic Signaling Domain of the Outer Membrane Iron Transporter FecA from Escherichia coli.
ComponentsIron(III) dicitrate transport protein fecA
KeywordsMEMBRANE PROTEIN / METAL TRANSPORT / protein NMR
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-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor ...: / 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-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / 3-Layer(bab) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fe(3+) dicitrate transport protein FecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsFerguson, A.D. / Amezcua, C.A. / Chelliah, Y. / Rosen, M.K. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Signal transduction pathway of TonB-dependent transporters.
Authors: Ferguson, A.D. / Amezcua, C.A. / Halabi, N.M. / Chelliah, Y. / Rosen, M.K. / Ranganathan, R. / Deisenhofer, J.
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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)8,3671
Polymers8,3671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1closest to average

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Components

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


Mass: 8367.117 Da / Num. of mol.: 1 / Fragment: N-terminal residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fecA / 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
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA

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Sample preparation

DetailsContents: 1mM protein / Solvent system: 50mM NaPi
Sample conditionsIonic strength: 50mM NaCl / pH: 6 / 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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio, F. et alprocessing
VNMR6.1CVariancollection
NMRView5.2.2Johnson, B. et aldata analysis
ARIA1.2Nilges, M. and O'Donoghue, S.I.structure solution
ARIA1.2Nilges, M. and O'Donoghue, S.I.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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