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- PDB-6q5e: Crystal structure of the ferric enterobactin receptor from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 6q5e
TitleCrystal structure of the ferric enterobactin receptor from Pseudomonas aeruginosa (PfeA) in complex with enterobactin
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor / protochelin
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-EB4 / : / Chem-LP5 / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
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
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: 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 24, 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

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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)79,9224
Polymers78,4851
Non-polymers1,4373
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-6 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.630, 159.260, 78.610
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: 78485.125 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-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin / Enterobactin


Mass: 669.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27N3O15
#4: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.41 Å3/Da / Density % sol: 63.96 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→85.63 Å / Num. obs: 30261 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 22
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m9b

5m9b


Resolution: 2.7→79.63 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.917 / SU B: 29.292 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24938 1531 5.1 %RANDOM
Rwork0.2079 ---
obs0.21002 28689 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.148 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2--3.35 Å20 Å2
3----5.33 Å2
Refinement stepCycle: 1 / Resolution: 2.7→79.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 83 33 5486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135571
X-RAY DIFFRACTIONr_bond_other_d00.0174922
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.6497544
X-RAY DIFFRACTIONr_angle_other_deg1.221.57711444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5755697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18622.347311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6915880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5091540
X-RAY DIFFRACTIONr_chiral_restr0.0510.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.026407
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021181
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_it3.3484.2882791
X-RAY DIFFRACTIONr_mcbond_other3.3474.2882790
X-RAY DIFFRACTIONr_mcangle_it4.7696.4443487
X-RAY DIFFRACTIONr_mcangle_other4.7696.4443488
X-RAY DIFFRACTIONr_scbond_it44.7752780
X-RAY DIFFRACTIONr_scbond_other44.7772781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7617.0064058
X-RAY DIFFRACTIONr_long_range_B_refined7.21949.5035807
X-RAY DIFFRACTIONr_long_range_B_other7.21949.5195808
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 107 -
Rwork0.31 2067 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -83.2885 Å / Origin y: 27.2603 Å / Origin z: 96.7043 Å
111213212223313233
T0.0733 Å2-0.0415 Å20.0354 Å2-0.0519 Å2-0.0654 Å2--0.2768 Å2
L1.1683 °20.3331 °20.3187 °2-2.588 °21.7654 °2--4.3704 °2
S-0.0434 Å °-0.0593 Å °-0.0382 Å °-0.4325 Å °0.261 Å °-0.226 Å °-0.2431 Å °0.3627 Å °-0.2175 Å °

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