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- PDB-6z33: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -

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Basic information

Entry
Database: PDB / ID: 6z33
TitleCrystal structure of the ferric enterobactin receptor (PfeA) in complex with BCV
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
: / Chem-Q62 / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.711 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 19, 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)79,3184
Polymers78,7441
Non-polymers5733
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 area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.962, 157.358, 78.077
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 PAO1 (bacteria) / Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098
#2: Chemical ChemComp-Q62 / ~{N}-[(5~{S})-5-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-6-oxidanylidene-6-(prop-2-ynylamino)hexyl]-2,3-bis(oxidanyl)benzamide


Mass: 455.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O7 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.711→78.679 Å / Num. obs: 24453 / % possible obs: 83 % / Redundancy: 7.5 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.9
Reflection shellResolution: 2.711→2.858 Å / Num. unique obs: 1224 / CC1/2: 0.555

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q5E

6q5e


Resolution: 2.711→78.679 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.934 / SU B: 33.775 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 1.199 / ESU R Free: 0.355
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2515 1171 4.789 %
Rwork0.2258 23282 -
all0.227 --
obs-24453 82.984 %
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: 101.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.445 Å20 Å20 Å2
2---0.945 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.711→78.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 38 0 5408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135525
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174877
X-RAY DIFFRACTIONr_ext_dist_refined_d0.020.018152
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6487485
X-RAY DIFFRACTIONr_angle_other_deg1.0731.57811328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6395697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68722.347311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11315880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2751540
X-RAY DIFFRACTIONr_chiral_restr0.0490.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.026378
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021178
X-RAY DIFFRACTIONr_nbd_refined0.2080.2951
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.24800
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22542
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.26
X-RAY DIFFRACTIONr_nbd_other0.3010.232
X-RAY DIFFRACTIONr_mcbond_it6.6487.4362791
X-RAY DIFFRACTIONr_mcbond_other6.6497.4362790
X-RAY DIFFRACTIONr_mcangle_it9.07611.1723487
X-RAY DIFFRACTIONr_mcangle_other9.07511.1713488
X-RAY DIFFRACTIONr_scbond_it7.1347.832734
X-RAY DIFFRACTIONr_scbond_other7.1227.832734
X-RAY DIFFRACTIONr_scangle_it9.49811.6033998
X-RAY DIFFRACTIONr_scangle_other9.49711.6033999
X-RAY DIFFRACTIONr_lrange_it12.081144.83923166
X-RAY DIFFRACTIONr_lrange_other12.08144.83723167
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
2.711-2.7810.464200.3893610.39321320.6820.69217.87050.385
2.781-2.8570.342410.3367860.33620780.8420.83239.79790.325
2.857-2.940.327700.31211100.31220230.8130.82158.32920.3
2.94-3.0310.317710.29813810.29919860.8410.84873.11180.284
3.031-3.130.256820.27416550.27319190.870.88190.51590.257
3.13-3.2390.236810.25417760.25318620.9140.89799.73150.227
3.239-3.3620.273780.23817110.2417890.8970.9021000.215
3.362-3.4990.294780.22716620.2317400.8840.9211000.203
3.499-3.6540.283840.22714530.2316460.9020.92993.37790.211
3.654-3.8320.261590.22112220.22316090.920.92679.61470.202
3.832-4.0380.266730.20314400.20615130.920.9361000.187
4.038-4.2830.232560.19213820.19414380.9340.9451000.183
4.283-4.5770.225710.19212980.19313710.9330.94999.85410.184
4.577-4.9430.188550.15912160.1612710.960.9671000.157
4.943-5.4120.262630.19211130.19511760.9470.9561000.187
5.412-6.0480.256460.21210260.21410720.9470.9521000.211
6.048-6.9760.262500.2089020.2119520.9290.9381000.22
6.976-8.5280.283330.2027960.2058300.8950.93699.87950.219
8.528-11.990.227380.2036170.2046550.9580.9611000.227
11.99-78.6790.236220.4613750.454050.9230.82298.02470.586
Refinement TLS params.Method: refined / Origin x: -83.517 Å / Origin y: 27.1096 Å / Origin z: 96.1277 Å
111213212223313233
T0.0341 Å2-0.0246 Å20.0302 Å2-0.0978 Å2-0.0378 Å2--0.0352 Å2
L1.5618 °20.3931 °20.272 °2-3.5797 °21.3778 °2--4.183 °2
S0.0493 Å °-0.0942 Å °-0.0084 Å °-0.2918 Å °0.1521 Å °-0.3195 Å °-0.2523 Å °0.2543 Å °-0.2014 Å °
Refinement TLS groupSelection: ALL

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