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- PDB-6y47: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -

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Basic information

Entry
Database: PDB / ID: 6y47
TitleCrystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV-L5
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / TONB dependent transporter / siderophore
Function / homology
Function and homology information


colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore transport / siderophore uptake transmembrane transporter activity / enterobactin transport / enterobactin transmembrane transporter activity / outer membrane / enterobactin binding / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / 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 / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
: / Chem-OWT / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsNaismith, J.H. / Moynie, L.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Hijacking of the Enterobactin Pathway by a Synthetic Catechol Vector Designed for Oxazolidinone Antibiotic Delivery in Pseudomonas aeruginosa.
Authors: Moynie, L. / Hoegy, F. / Milenkovic, S. / Munier, M. / Paulen, A. / Gasser, V. / Faucon, A.L. / Zill, N. / Naismith, J.H. / Ceccarelli, M. / Schalk, I.J. / Mislin, G.L.A.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric enterobactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8254
Polymers78,7441
Non-polymers1,0813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-11 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.010, 156.951, 77.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Ferric enterobactin receptor


Mass: 78744.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098
#2: Chemical ChemComp-OWT / ~{N}-[(5~{S})-6-azanyl-5-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-6-oxidanylidene-hexyl]-2,3-bis(oxidanyl)benzamide


Mass: 962.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H55FN10O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG 8000 ADA Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.037→156.95 Å / Num. obs: 20933 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 116.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.3
Reflection shellResolution: 3.037→3.09 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 982 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q5E

6q5e


Resolution: 3.04→69.54 Å / SU ML: 0.5766 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0801 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 1019 4.88 %
Rwork0.2184 19856 -
obs0.2208 20875 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 125.25 Å2
Refinement stepCycle: LAST / Resolution: 3.04→69.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 35 0 5405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245516
X-RAY DIFFRACTIONf_angle_d0.5557482
X-RAY DIFFRACTIONf_chiral_restr0.042794
X-RAY DIFFRACTIONf_plane_restr0.0042999
X-RAY DIFFRACTIONf_dihedral_angle_d8.28293252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.20.45451460.38062760X-RAY DIFFRACTION98.38
3.2-3.40.35541470.2762764X-RAY DIFFRACTION99.86
3.4-3.660.29711490.23262793X-RAY DIFFRACTION99.93
3.66-4.030.30531490.22652814X-RAY DIFFRACTION100
4.03-4.610.24161260.19332861X-RAY DIFFRACTION100
4.61-5.810.23231490.19922861X-RAY DIFFRACTION100
5.81-69.540.25381530.21443003X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: -83.547387746 Å / Origin y: 27.2777616146 Å / Origin z: 95.670816 Å
111213212223313233
T0.676119873049 Å2-0.045186349828 Å20.0468608918937 Å2-0.765232845458 Å2-0.0757591929896 Å2--0.795099159911 Å2
L1.83772080606 °20.371954916191 °20.365238575568 °2-4.41945846668 °21.45541607243 °2--4.56767176467 °2
S0.192747016887 Å °-0.277522432472 Å °0.0428273956682 Å °-0.180950442177 Å °0.068698839823 Å °-0.306969239405 Å °-0.152330633144 Å °0.20898510387 Å °-0.18391246949 Å °
Refinement TLS groupSelection details: (chain A and resseq 24:901)

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