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- PDB-6z2n: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -

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Basic information

Entry
Database: PDB / ID: 6z2n
TitleCrystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV-L6
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 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
: / BCV-L6 / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.029 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
DepositionMay 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 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 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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)79,7534
Polymers78,7441
Non-polymers1,0093
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-11 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.240, 156.625, 77.492
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: 78744.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-Q5N / BCV-L6 / [4-[[[(2~{S})-2,6-bis[[2,3-bis(oxidanyl)phenyl]carbonylamino]hexanoyl]amino]methyl]-1,2,3-triazol-1-yl]methyl 4-[4-[(5~{R})-5-(acetamidomethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]-2-fluoranyl-phenyl]piperazine-1-carboxylate


Mass: 890.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H47FN10O12 / Feature type: SUBJECT OF INVESTIGATION
#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: 3.43 Å3/Da / Density % sol: 64.18 %
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: 3.029→86.24 Å / Num. obs: 21109 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.5
Reflection shellResolution: 3.03→3.08 Å / Num. unique obs: 1019 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q5e

6q5e


Resolution: 3.029→75.66 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.93 / SU B: 50.249 / SU ML: 0.373 / Cross valid method: NONE / ESU R Free: 0.42
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2623 1031 4.894 %
Rwork0.2205 20036 -
all0.223 --
obs-21067 99.82 %
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: 122.234 Å2
Baniso -1Baniso -2Baniso -3
1-3.667 Å20 Å20 Å2
2---4.11 Å20 Å2
3---0.444 Å2
Refinement stepCycle: LAST / Resolution: 3.029→75.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 35 0 5405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135522
X-RAY DIFFRACTIONr_bond_other_d0.0040.0174873
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0780.018683
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.6487482
X-RAY DIFFRACTIONr_angle_other_deg1.1181.57811320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7335697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39222.468308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38415880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591540
X-RAY DIFFRACTIONr_chiral_restr0.0480.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.026375
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021177
X-RAY DIFFRACTIONr_nbd_refined0.2220.2963
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24883
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22518
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2158
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.28
X-RAY DIFFRACTIONr_nbd_other0.2750.229
X-RAY DIFFRACTIONr_mcbond_it5.6468.9232791
X-RAY DIFFRACTIONr_mcbond_other5.6478.9232790
X-RAY DIFFRACTIONr_mcangle_it8.24713.4023487
X-RAY DIFFRACTIONr_mcangle_other8.24613.4023488
X-RAY DIFFRACTIONr_scbond_it6.4469.4282731
X-RAY DIFFRACTIONr_scbond_other6.3819.4272731
X-RAY DIFFRACTIONr_scangle_it9.17213.9613995
X-RAY DIFFRACTIONr_scangle_other9.17113.9613996
X-RAY DIFFRACTIONr_lrange_it11.358190.47611944
X-RAY DIFFRACTIONr_lrange_other11.357190.46611945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.029-3.1070.417720.3581440X-RAY DIFFRACTION97.8641
3.107-3.1920.367790.3281416X-RAY DIFFRACTION100
3.192-3.2850.316690.2941363X-RAY DIFFRACTION100
3.285-3.3860.33800.2681340X-RAY DIFFRACTION100
3.386-3.4970.328710.2441297X-RAY DIFFRACTION100
3.497-3.6190.235580.2321270X-RAY DIFFRACTION100
3.619-3.7550.261690.2261212X-RAY DIFFRACTION99.922
3.755-3.9080.301680.2231166X-RAY DIFFRACTION100
3.908-4.0820.252540.2091149X-RAY DIFFRACTION100
4.082-4.2810.267530.1951068X-RAY DIFFRACTION100
4.281-4.5120.208430.1751057X-RAY DIFFRACTION99.9092
4.512-4.7840.185460.156978X-RAY DIFFRACTION100
4.784-5.1140.207500.158932X-RAY DIFFRACTION100
5.114-5.5220.251450.178862X-RAY DIFFRACTION100
5.522-6.0460.306350.205806X-RAY DIFFRACTION100
6.046-6.7560.311370.195736X-RAY DIFFRACTION100
6.756-7.7930.262360.192661X-RAY DIFFRACTION100
7.793-9.5250.231270.196557X-RAY DIFFRACTION100
9.525-13.3890.196240.222446X-RAY DIFFRACTION100
13.389-75.660.359150.414280X-RAY DIFFRACTION98.9933
Refinement TLS params.Method: refined / Origin x: -83.213 Å / Origin y: 26.9742 Å / Origin z: 95.2489 Å
111213212223313233
T0.0505 Å2-0.0315 Å20.0356 Å2-0.0376 Å2-0.0164 Å2--0.0516 Å2
L2.0388 °20.3572 °20.2115 °2-4.9386 °21.1195 °2--4.453 °2
S0.0811 Å °-0.2272 Å °0.0559 Å °-0.1951 Å °-0.0171 Å °-0.342 Å °-0.3546 Å °0.1758 Å °-0.064 Å °
Refinement TLS groupSelection: ALL

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