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- PDB-2a02: Solution NMR Structure of the Periplasmic Signaling Domain of the... -

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Basic information

Entry
Database: PDB / ID: 2a02
TitleSolution NMR Structure of the Periplasmic Signaling Domain of the Outer Membrane Iron Transporter PupA from Pseudomonas putida.
ComponentsFerric-pseudobactin 358 receptor
KeywordsMEMBRANE PROTEIN / METAL TRANSPORT / protein NMR
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane => GO:0016020
Similarity search - Function
TonB-dependent receptor-like / 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-like / 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, 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
Ferric-pseudobactin 358 receptor
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
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 15, 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ferric-pseudobactin 358 receptor


Theoretical massNumber of molelcules
Total (without water)8,7521
Polymers8,7521
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 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ferric-pseudobactin 358 receptor


Mass: 8751.724 Da / Num. of mol.: 1 / Fragment: N-terminal residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pupA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P25184

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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

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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 the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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