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- PDB-6i98: Structure of the ferrioxamine B transporter FoxA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6i98
TitleStructure of the ferrioxamine B transporter FoxA from Pseudomonas aeruginosa, apo state
ComponentsFerric hydroxamate uptake
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


nickel cation transport / siderophore-iron import into cell / zinc ion transport / siderophore transport / siderophore uptake transmembrane transporter activity / outer membrane / cell outer membrane / signaling receptor activity / cell surface receptor signaling pathway
Similarity search - Function
Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / 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
3-HYDROXY-TETRADECANOIC ACID / NICKEL (II) ION / Metal-pseudopaline receptor CntO / Metal-pseudopaline receptor CntO
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric hydroxamate uptake
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00727
Polymers75,4221
Non-polymers3,58526
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-153 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.554, 174.554, 180.245
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferric hydroxamate uptake / Ferrichrome-iron receptor / Ferrioxamine receptor FoxA / TonB-dependent siderophore receptor


Mass: 75421.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: fhuA, fhuA_5, C0044_18480, CAZ10_13360, CCBH4851_00003, DZ940_30305, EGY23_22030, PAERUG_E15_London_28_01_14_03466
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CQY7, UniProt: Q9I116*PLUS

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Non-polymers , 7 types, 40 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.24 Å3/Da / Density % sol: 76.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium sulfate, 0.1M HEPES pH 7.4

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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: 1.03332 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03332 Å / Relative weight: 1
ReflectionResolution: 2.8→48.53 Å / Num. obs: 40394 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.092 / Rrim(I) all: 0.226 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.91 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4492 / CC1/2: 0.547 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→151.17 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.892 / SU B: 24.424 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 2028 5 %RANDOM
Rwork0.2133 ---
obs0.2156 38331 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141 Å2 / Biso mean: 58.049 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----1.81 Å2
Refinement stepCycle: final / Resolution: 2.8→151.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 193 14 5532
Biso mean--92.28 50.97 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195619
X-RAY DIFFRACTIONr_bond_other_d0.0020.024956
X-RAY DIFFRACTIONr_angle_refined_deg2.341.977588
X-RAY DIFFRACTIONr_angle_other_deg1.151311522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8485676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72924.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6915858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.751535
X-RAY DIFFRACTIONr_chiral_restr0.1290.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026253
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021186
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 155 -
Rwork0.328 2769 -
all-2924 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -6.7742 Å / Origin y: -70.3826 Å / Origin z: -12.8859 Å
111213212223313233
T0.0501 Å2-0.0038 Å20.055 Å2-0.0095 Å2-0.0236 Å2--0.1555 Å2
L0.4411 °2-0.0844 °2-0.0222 °2-0.4744 °2-0.0385 °2--0.4213 °2
S0.023 Å °-0.0574 Å °0.0847 Å °-0.0016 Å °-0.0017 Å °-0.0176 Å °-0.1202 Å °-0.0082 Å °-0.0213 Å °

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