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- PDB-5nc3: Crystal structure of the ferric enterobactin receptor (PfeA) from... -

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Basic information

Entry
Database: PDB / ID: 5nc3
TitleCrystal structure of the ferric enterobactin receptor (PfeA) from Pseudomonas aeruginosa in complex with the tris-catechol vector
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor
Function / homology
Function and homology information


enterobactin transmembrane transporter activity / enterobactin transport / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / siderophore transport / outer membrane / enterobactin binding / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor (TBDR) proteins profile. / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
Chem-8SW / : / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.57 Å
AuthorsMoynie, L. / Naismith, J.H.
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
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: 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

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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)79,4933
Polymers78,7441
Non-polymers7482
Water181
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.697, 155.171, 77.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8SW / ~{N}-[2-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-3-oxidanylidene-3-(prop-2-ynylamino)propyl]amino]-3-oxidanylidene-propyl]amino]-2-oxidanylidene-ethyl]-2,3-bis(oxidanyl)benzamide


Mass: 692.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H32N6O12
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG 8000 ADA Magnesium acetate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.57→77.8 Å / Num. obs: 34110 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.1
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.148 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3283 / CC1/2: 0.756 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.57→77.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 34.521 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R: 0.414 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26285 1728 5.1 %RANDOM
Rwork0.21881 ---
obs0.22103 32378 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 97.309 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20 Å20 Å2
2--8.31 Å20 Å2
3----4.93 Å2
Refinement stepCycle: 1 / Resolution: 2.57→77.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5421 0 51 1 5473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025591
X-RAY DIFFRACTIONr_bond_other_d0.0010.025105
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9557579
X-RAY DIFFRACTIONr_angle_other_deg0.6763.00211718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.945704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29224.391271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48915888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7961540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021335
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7985.3332822
X-RAY DIFFRACTIONr_mcbond_other4.7975.3352823
X-RAY DIFFRACTIONr_mcangle_it6.4648.0053524
X-RAY DIFFRACTIONr_mcangle_other6.4658.0073525
X-RAY DIFFRACTIONr_scbond_it5.65.8252769
X-RAY DIFFRACTIONr_scbond_other5.65.8272770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7468.5734056
X-RAY DIFFRACTIONr_long_range_B_refined10.40223277
X-RAY DIFFRACTIONr_long_range_B_other10.40123278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 123 -
Rwork0.43 2349 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
125.3954-5.6772-19.38911.29044.324414.8344-0.8452-0.7818-0.56950.22080.27960.09730.69410.55590.56560.71950.0481-0.05640.5639-0.00870.728-13.444220.0131-0.5327
23.40940.2356-0.84442.0111-0.46226.17160.16240.3629-0.31480.3582-0.0960.12580.37590.3246-0.06640.11180.040.02310.10970.02190.179-1.700326.7929-13.9147
33.0589-0.014-1.13732.14020.39646.38330.09560.00960.1680.1497-0.2042-0.3097-0.45791.54070.10850.0815-0.0987-0.05670.49540.12220.319912.742733.3706-14.2804
462.172812.4384-25.43762.5512-3.718440.93650.4248-2.8298-0.17630.1194-0.5789-0.0310.19170.66710.15410.97420.01760.28470.2263-0.15140.6648-7.812145.6239.4526
56.071-0.4927-4.48391.3910.83989.82050.3657-0.05560.53260.141-0.15480.0307-1.11590.5691-0.21090.1764-0.09480.05120.1090.10480.34630.646339.9524-14.9182
63.962-0.3258-1.69581.6253-0.25397.52320.31860.65930.43980.17560.00840.1971-0.9176-0.0517-0.3270.13360.02750.04840.13810.14370.3291-7.141939.7272-18.5834
72.5825-0.4913-0.261.8106-0.84184.05510.05870.7243-0.38320.03910.14740.41780.5487-0.5887-0.20610.0993-0.0417-0.00120.3178-0.02860.3769-14.420124.8527-21.3012
82.4583-0.32441.45532.2789-2.46987.7820.18620.465-0.6075-0.2167-0.10650.18111.15320.2313-0.07970.56250.20180.04770.2396-0.17760.51352.124212.2371-20.1543
92.7678-0.5288-0.12313.5582-0.34832.09530.2050.5535-0.3697-0.0485-0.5054-0.69790.9791.18560.30040.49040.5940.08360.85130.06760.357114.100419.3477-18.2459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 30
2X-RAY DIFFRACTION2A31 - 154
3X-RAY DIFFRACTION3A155 - 239
4X-RAY DIFFRACTION4A240 - 244
5X-RAY DIFFRACTION5A245 - 302
6X-RAY DIFFRACTION6A303 - 358
7X-RAY DIFFRACTION7A359 - 587
8X-RAY DIFFRACTION8A588 - 646
9X-RAY DIFFRACTION9A647 - 722

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