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- PDB-7obw: Crystal structure of the ferric enterobactin receptor (PfeA) from... -

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Basic information

Entry
Database: PDB / ID: 7obw
TitleCrystal structure of the ferric enterobactin receptor (PfeA) from Pseudomonas aeruginosa in complex with TCV-L6
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / siderophore transporter
Function / homology
Function and homology information


colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / siderophore transport / enterobactin transport / enterobactin transmembrane transporter activity / outer membrane / enterobactin binding / cell outer membrane / signaling receptor activity
Similarity search - Function
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 / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
Similarity search - Domain/homology
: / Chem-V82 / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme
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
DepositionApr 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.2Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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
AAA: Ferric enterobactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8535
Polymers78,4851
Non-polymers2,3684
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area28900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.414, 157.114, 77.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ferric enterobactin receptor


Mass: 78485.125 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-V82 / [4-[[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-[2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]ethanoylamino]propanoyl]amino]propanoyl]amino]methyl]-1,2,3-triazol-1-yl]methyl 4-[4-[(5~{S})-5-(acetamidomethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]-2-fluoranyl-phenyl]piperazine-1-carboxylate


Mass: 1128.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H54FN13O17 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.51 Å3/Da / Density % sol: 64.97 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.659→58.43 Å / Num. obs: 31558 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13
Reflection shellResolution: 2.66→2.7 Å / Num. unique obs: 1486 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q5e

6q5e


Resolution: 2.66→58.43 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.78 / SU ML: 0.308 / Cross valid method: FREE R-VALUE / ESU R: 0.518 / ESU R Free: 0.321
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2767 1539 4.885 %
Rwork0.2306 29965 -
all0.233 --
obs-31504 99.778 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 88.431 Å2
Baniso -1Baniso -2Baniso -3
1-3.988 Å20 Å20 Å2
2---1.22 Å20 Å2
3----2.768 Å2
Refinement stepCycle: LAST / Resolution: 2.66→58.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 132 1 5496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135613
X-RAY DIFFRACTIONr_bond_other_d00.0174914
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0520.018135
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.687620
X-RAY DIFFRACTIONr_angle_other_deg1.1521.59811419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3125696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86222.468308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47215879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8641540
X-RAY DIFFRACTIONr_chiral_restr0.050.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.026513
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021217
X-RAY DIFFRACTIONr_nbd_refined0.2040.2889
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24558
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22528
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.219
X-RAY DIFFRACTIONr_nbd_other0.290.249
X-RAY DIFFRACTIONr_mcbond_it11.1479.2012791
X-RAY DIFFRACTIONr_mcbond_other11.1449.1982790
X-RAY DIFFRACTIONr_mcangle_it14.13413.8123484
X-RAY DIFFRACTIONr_mcangle_other14.12813.8123484
X-RAY DIFFRACTIONr_scbond_it11.58710.1252822
X-RAY DIFFRACTIONr_scbond_other11.58510.1272823
X-RAY DIFFRACTIONr_scangle_it15.66814.8994136
X-RAY DIFFRACTIONr_scangle_other15.66614.9014137
X-RAY DIFFRACTIONr_lrange_it16.939188.85311510
X-RAY DIFFRACTIONr_lrange_other16.939188.85511511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.7280.3921140.3742109X-RAY DIFFRACTION97.5856
2.728-2.8020.3971090.3672118X-RAY DIFFRACTION99.9551
2.802-2.8830.3811150.3342061X-RAY DIFFRACTION99.9541
2.883-2.9720.39890.3082038X-RAY DIFFRACTION100
2.972-3.0690.34930.2951942X-RAY DIFFRACTION99.9509
3.069-3.1760.349920.2691899X-RAY DIFFRACTION99.8997
3.176-3.2960.286980.2421814X-RAY DIFFRACTION99.9477
3.296-3.430.3081020.2421769X-RAY DIFFRACTION99.9466
3.43-3.5820.287940.2411681X-RAY DIFFRACTION100
3.582-3.7560.289880.241620X-RAY DIFFRACTION99.9415
3.756-3.9580.34750.2211550X-RAY DIFFRACTION100
3.958-4.1970.275710.2091483X-RAY DIFFRACTION100
4.197-4.4850.259760.1941379X-RAY DIFFRACTION100
4.485-4.8420.219660.1661300X-RAY DIFFRACTION100
4.842-5.3010.22570.191204X-RAY DIFFRACTION100
5.301-5.920.205570.2271090X-RAY DIFFRACTION100
5.92-6.8250.253490.207976X-RAY DIFFRACTION99.9025
6.825-8.330.268500.186832X-RAY DIFFRACTION100
8.33-11.6620.211300.204677X-RAY DIFFRACTION100
11.662-58.4290.362140.349422X-RAY DIFFRACTION99.5434

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