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- PDB-6i97: Structure of the ferrioxamine B transporter FoxA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6i97
TitleStructure of the ferrioxamine B transporter FoxA from Pseudomonas aeruginosa in complex with ferrioxamine B and a C-terminal TonB fragment
Components
  • Protein TonB
  • TonB-dependent receptor
KeywordsMEMBRANE PROTEIN / outer membrane protein iron uptake
Function / homology
Function and homology information


energy transducer activity / type IV pilus-dependent motility / iron import into cell / siderophore-iron import into cell / siderophore transport / siderophore uptake transmembrane transporter activity / outer membrane / plasma membrane protein complex / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation ...energy transducer activity / type IV pilus-dependent motility / iron import into cell / siderophore-iron import into cell / siderophore transport / siderophore uptake transmembrane transporter activity / outer membrane / plasma membrane protein complex / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / cellular response to antibiotic / cell outer membrane / transmembrane transport / protein transport / signaling receptor activity / outer membrane-bounded periplasmic space / cell surface receptor signaling pathway / plasma membrane
Similarity search - Function
TonB-dependent receptor-like / TolA/TonB C-terminal domain / TonB / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / Secretin/TonB, short N-terminal domain ...TonB-dependent receptor-like / TolA/TonB C-terminal domain / TonB / Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / Maltoporin; Chain A / 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 / Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ferrioxamine B / Protein TonB / TonB-dependent receptor / Protein TonB / Ferrioxamine receptor FoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsJosts, I. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Elife / Year: 2019
Title: Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake.
Authors: Josts, I. / Veith, K. / Tidow, H.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TonB-dependent receptor
B: TonB-dependent receptor
D: Protein TonB
E: Protein TonB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,0366
Polymers190,8094
Non-polymers1,2272
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-33 kcal/mol
Surface area65710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.639, 174.404, 214.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TonB-dependent receptor


Mass: 84943.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: optS, NCTC13621_01915 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A485EWC9, UniProt: Q9I116*PLUS
#2: Protein Protein TonB


Mass: 10461.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CSB93_1183 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3J1C6, UniProt: Q51368*PLUS
#3: Chemical ChemComp-0UE / Ferrioxamine B


Mass: 613.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H45FeN6O8
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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.8M Ammonium sulfate, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.35→48.84 Å / Num. obs: 88597 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.13 / Net I/σ(I): 5.6
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1 / Num. unique obs: 4510 / CC1/2: 0.389 / Rpim(I) all: 0.848 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→135.22 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.782 / SU B: 43.383 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 4361 4.9 %RANDOM
Rwork0.2294 ---
obs0.2311 84137 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.63 Å2 / Biso mean: 86.715 Å2 / Biso min: 46.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 3.35→135.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13362 0 80 0 13442
Biso mean--78.32 --
Num. residues----1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01913749
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212253
X-RAY DIFFRACTIONr_angle_refined_deg2.5411.95718638
X-RAY DIFFRACTIONr_angle_other_deg1.256328416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.96751695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27623.911693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.999152201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.46715104
X-RAY DIFFRACTIONr_chiral_restr0.1290.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02115585
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022959
LS refinement shellResolution: 3.35→3.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 327 -
Rwork0.344 6117 -
all-6444 -
obs--99.95 %
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)
10.2652-0.1170.02730.7360.92971.31290.00630.02210.03030.0935-0.13440.07240.1787-0.20960.12810.1776-0.14620.10060.1375-0.03790.2362-18.2802-9.184262.4393
20.9299-0.34330.85680.1869-0.27181.4397-0.0235-0.03050.09110.0443-0.04820.0297-0.0859-0.04420.07180.0579-0.0731-0.02720.11380.04680.3149-45.2268-39.86636.6866
31.6995-0.4196-1.63643.91331.15722.13210.0504-0.23030.16530.1475-0.0117-0.1545-0.1380.1842-0.03870.0515-0.0312-0.04260.1463-0.0470.20825.1836-38.257936.9308
44.401-1.18082.26341.8136-0.80822.48660.0714-0.0652-0.0886-0.12940.00690.0950.2886-0.228-0.07830.0969-0.02070.00220.04930.02130.1825-14.0201-59.793432.2134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 820
2X-RAY DIFFRACTION2B53 - 820
3X-RAY DIFFRACTION3D251 - 340
4X-RAY DIFFRACTION4E251 - 340

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