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- PDB-5nc4: Crystal structure of the ferric enterobactin receptor (PfeA) in c... -

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Basic information

Entry
Database: PDB / ID: 5nc4
TitleCrystal structure of the ferric enterobactin receptor (PfeA) in complex with protochelin from Pseudomonas aeruginosa
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor / protochelin
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-8T2 / : / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoynie, L. / Naismith, J.H.
CitationJournal: Nat Commun / Year: 2019
Title: The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model.
Authors: Moynie, L. / Milenkovic, S. / Mislin, G.L.A. / Gasser, V. / Malloci, G. / Baco, E. / McCaughan, R.P. / Page, M.G.P. / Schalk, I.J. / Ceccarelli, M. / Naismith, J.H.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)79,4253
Polymers78,7441
Non-polymers6802
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.751, 157.352, 78.108
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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-8T2 / ~{N}-[(5~{S})-5-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-6-[4-[[2,3-bis(oxidanyl)phenyl]carbonylamino]butylamino]-6-oxidanylidene-hexyl]-2,3-bis(oxidanyl)benzamide


Mass: 624.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H36N4O10
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: 3.39 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000, ADA, Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→157.35 Å / Num. obs: 26955 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.5
Reflection shellResolution: 2.8→2.813 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 245 / CC1/2: 0.867 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M9K

5m9k
PDB Unreleased entry


Resolution: 2.8→78.68 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.907 / SU B: 34.381 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.345 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26326 1310 4.9 %RANDOM
Rwork0.21811 ---
obs0.22026 25602 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 110.265 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å20 Å2
2--2.15 Å20 Å2
3----4.61 Å2
Refinement stepCycle: 1 / Resolution: 2.8→78.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 46 0 5409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025528
X-RAY DIFFRACTIONr_bond_other_d0.0010.025058
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9557491
X-RAY DIFFRACTIONr_angle_other_deg0.7083.00211612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5065696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95224.328268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.115879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5491540
X-RAY DIFFRACTIONr_chiral_restr0.0970.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216491
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021323
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_it5.5966.0862790
X-RAY DIFFRACTIONr_mcbond_other5.5716.0842790
X-RAY DIFFRACTIONr_mcangle_it7.5839.1463484
X-RAY DIFFRACTIONr_mcangle_other7.5369.1423483
X-RAY DIFFRACTIONr_scbond_it6.0956.542738
X-RAY DIFFRACTIONr_scbond_other6.0946.5412739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3989.6574008
X-RAY DIFFRACTIONr_long_range_B_refined11.03123137
X-RAY DIFFRACTIONr_long_range_B_other11.03123138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 105 -
Rwork0.356 1836 -
obs--100 %
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)
17.5386-1.47470.84177.2906-0.9936.60250.23940.4075-0.8608-0.7659-0.09550.06290.2846-0.1152-0.14390.2062-0.0463-0.00970.053-0.04250.2639-0.9632177.7158165.0622
22.27530.61930.19073.37361.22216.10070.132-0.1734-0.0281-0.57220.0777-0.311-0.42640.1156-0.20970.1334-0.040.07930.0638-0.05750.22332.0168186.7669169.94
32.82480.4114-0.84283.7327-0.35657.2190.0785-0.03320.3797-0.38050.04040.4604-0.8167-1.1793-0.11890.15410.1492-0.0450.2488-0.10730.4102-11.227191.6533172.4318
42.47260.36410.43113.74591.52464.10930.2502-0.28210.5326-0.4430.027-0.1976-1.79540.1394-0.27720.8825-0.09980.17130.0726-0.14050.38731.6456198.1192173.4973
52.24090.30240.3672.88780.56525.08760.0601-0.0165-0.106-0.55370.3617-0.9029-0.5031.4061-0.42180.1477-0.19590.19850.5483-0.22990.707518.9806190.0556172.1911
61.44810.86960.65574.48482.50454.94970.2521-0.4654-0.39210.15790.2892-0.94640.77520.6795-0.54130.18250.0565-0.06680.37470.00130.530611.2218177.7444180.8878
72.33680.58250.98093.30332.88517.07780.1966-0.2228-0.50610.219-0.0595-0.23651.14430.0824-0.13710.4344-0.1136-0.01050.20590.09830.432-2.1885170.0586176.7408
82.5845-0.25220.90253.91980.59335.00220.3261-0.2752-0.2964-0.1616-0.34190.67780.5336-1.12470.01580.1019-0.1033-0.00370.4241-0.05950.4062-13.8836177.4903174.4992
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 63
2X-RAY DIFFRACTION2A64 - 165
3X-RAY DIFFRACTION3A166 - 240
4X-RAY DIFFRACTION4A241 - 335
5X-RAY DIFFRACTION5A336 - 447
6X-RAY DIFFRACTION6A448 - 586
7X-RAY DIFFRACTION7A587 - 645
8X-RAY DIFFRACTION8A646 - 721

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