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- PDB-2m6l: Solution structure of the Escherichia coli holo ferric enterobact... -

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Basic information

Entry
Database: PDB / ID: 2m6l
TitleSolution structure of the Escherichia coli holo ferric enterobactin binding protein
ComponentsFerrienterobactin-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / periplasmic / siderophore
Function / homology
Function and homology information


ferric-enterobactin import into cell / iron import into cell / Iron assimilation using enterobactin / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / DNA damage response / membrane
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ferric enterobactin-binding periplasmic protein FepB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsChu, B.C.H. / Otten, R. / Krewulak, K.D. / Mulder, F.A.A. / Vogel, H.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The solution structure, binding properties, and dynamics of the bacterial siderophore-binding protein FepB.
Authors: Chu, B.C. / Otten, R. / Krewulak, K.D. / Mulder, F.A. / Vogel, H.J.
History
DepositionApr 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrienterobactin-binding periplasmic protein


Theoretical massNumber of molelcules
Total (without water)34,3701
Polymers34,3701
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ferrienterobactin-binding periplasmic protein


Mass: 34370.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0592, fepB, JW0584 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEL6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 1H-15N NOESY
1213D 1H-13C NOESY
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CO)CA
1713D HNCA
1812D 1H-15N HSQC

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Sample preparation

Details
Solution-IDSolvent system
193% H2O/7% D2O
293% H2O/7% D2O
393% H2O/7% D2O
Sample conditionsIonic strength: 0 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR softwareName: X-PLOR NIH / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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