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- PDB-6yy5: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -

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Basic information

Entry
Database: PDB / ID: 6yy5
TitleCrystal structure of the ferric enterobactin receptor (PfeA) in complex with TCV_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-QDQ / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.717 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 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: 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 1.3Oct 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)80,0003
Polymers78,7441
Non-polymers1,2562
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.795, 157.049, 77.503
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-QDQ / ~{N}-[2-[[(2~{S})-3-[[(2~{S})-3-[[1-[2-[2-[2-[4-[4-[5-(acetamidomethyl)-2-oxidanylidene-1,3-oxazolidin-3-yl]-2-fluoranyl-phenyl]piperazin-1-yl]-2-oxidanylidene-ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]methylamino]-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-oxidanylidene-propyl]amino]-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-oxidanylidene-propyl]amino]-2-oxidanylidene-ethyl]-2,3-bis(oxidanyl)benzamide


Mass: 1200.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H62FN13O18 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
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: 2.717→75.293 Å / Num. obs: 28920 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.5
Reflection shellResolution: 2.717→2.76 Å / Rmerge(I) obs: 1.752 / Num. unique obs: 1334 / CC1/2: 0.443 / % possible all: 93.5

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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: 2.717→75.293 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.933 / SU B: 32.532 / SU ML: 0.28 / Cross valid method: NONE / ESU R: 0.58 / ESU R Free: 0.318
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 1465 5.075 %
Rwork0.2144 --
all0.216 --
obs-28865 99.634 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 95.139 Å2
Baniso -1Baniso -2Baniso -3
1-1.126 Å20 Å20 Å2
2---0.961 Å20 Å2
3----0.165 Å2
Refinement stepCycle: LAST / Resolution: 2.717→75.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 50 7 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174871
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0550.018145
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.6487508
X-RAY DIFFRACTIONr_angle_other_deg1.1741.57711321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5275697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3622.468308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75715880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4731540
X-RAY DIFFRACTIONr_chiral_restr0.0520.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.026408
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021184
X-RAY DIFFRACTIONr_nbd_refined0.2080.2954
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.24706
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22532
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.25
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3980.28
X-RAY DIFFRACTIONr_nbd_other0.340.225
X-RAY DIFFRACTIONr_mcbond_it5.4846.5362791
X-RAY DIFFRACTIONr_mcbond_other5.4856.5362790
X-RAY DIFFRACTIONr_mcangle_it7.3949.8243487
X-RAY DIFFRACTIONr_mcangle_other7.3939.8253488
X-RAY DIFFRACTIONr_scbond_it6.1887.0312742
X-RAY DIFFRACTIONr_scbond_other6.1757.0312740
X-RAY DIFFRACTIONr_scangle_it8.62310.3744021
X-RAY DIFFRACTIONr_scangle_other8.62210.3754022
X-RAY DIFFRACTIONr_lrange_it9.82136.21911522
X-RAY DIFFRACTIONr_lrange_other9.82136.21711522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.717-2.7880.3681030.37919170.37821170.6290.62495.4180.375
2.788-2.8640.3921090.33119410.33520520.7630.76199.90250.32
2.864-2.9470.3051100.30118630.30119760.8280.8399.84820.282
2.947-3.0370.3421040.28218390.28519430.8380.8721000.258
3.037-3.1370.341050.26117910.26518970.8460.89699.94730.233
3.137-3.2470.275960.22417250.22718210.9110.9251000.197
3.247-3.3690.245830.2116810.21217650.9230.93599.94330.189
3.369-3.5060.2791100.21115890.21516990.9160.9361000.193
3.506-3.6620.256660.20915610.21116270.9250.9381000.197
3.662-3.840.265810.21214900.21515710.9160.9321000.201
3.84-4.0470.216660.19414140.19514800.9370.9441000.185
4.047-4.2920.241600.1813800.18214400.9290.9561000.177
4.292-4.5870.243520.18712810.18913330.9290.9521000.185
4.587-4.9530.245770.1811550.18412320.9270.9511000.181
4.953-5.4230.222590.19111090.19311680.9430.9551000.194
5.423-6.060.252530.20810020.2110550.9440.9591000.212
6.06-6.990.257440.1968970.1999410.9340.9521000.204
6.99-8.5420.25430.1777670.1818100.9260.9591000.189
8.542-12.0030.184310.1836120.1836430.960.9621000.201
12.003-75.2930.318130.3483860.3463990.9680.8511000.39
Refinement TLS params.Method: refined / Origin x: -83.4932 Å / Origin y: 27.057 Å / Origin z: 95.3847 Å
111213212223313233
T0.0795 Å2-0.0466 Å20.0606 Å2-0.0647 Å2-0.0393 Å2--0.0507 Å2
L1.6976 °20.3767 °20.2187 °2-3.706 °21.3559 °2--4.0188 °2
S0.0613 Å °-0.1572 Å °0.025 Å °-0.4467 Å °0.1303 Å °-0.3753 Å °-0.2542 Å °0.2646 Å °-0.1916 Å °
Refinement TLS groupSelection: ALL

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