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- PDB-8rm3: Crystal structure of ferrioxamine transporter FoxA -

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Basic information

Entry
Database: PDB / ID: 8rm3
TitleCrystal structure of ferrioxamine transporter FoxA
ComponentsFerrioxamine receptor FoxA
KeywordsMEMBRANE PROTEIN / TonB-dependent transporter Siderophore
Function / homology
Function and homology information


siderophore-iron import into cell / 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
: / AMMONIUM ION / Ferrioxamine receptor FoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsJosts, I. / Tidow, H. / Mislin, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Crystal structure of ferrioxamine transporter FoxA
Authors: Josts, I. / Tidow, H. / Gaetan, M.
History
DepositionJan 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrioxamine receptor FoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,67519
Polymers90,0581
Non-polymers3,61718
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-22 kcal/mol
Surface area26690 Å2
Unit cell
Length a, b, c (Å)94.027, 94.027, 178.065
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Ferrioxamine receptor FoxA


Mass: 90058.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: foxA, PA2466 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I116
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 8 types, 151 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-A1H1T / [5-[2-(dipyridin-2-ylamino)ethanoylamino]pentyl-[4-[5-[[4-[5-[ethanoyl(oxidanyl)amino]pentylamino]-4-oxidanylidene-butanoyl]-oxidanyl-amino]pentylamino]-4-oxidanylidene-butanoyl]amino]oxyiron


Mass: 826.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H56FeN9O9 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1 M Ammonium sulphate 0.1 M HEPES pH 7.5 0.7% n-octyl-beta-d-glucoside

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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: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.22→81.43 Å / Num. obs: 37981 / % possible obs: 94.8 % / Redundancy: 94.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.028 / Rrim(I) all: 0.11 / Net I/σ(I): 16.1
Reflection shellResolution: 2.221→2.387 Å / Rmerge(I) obs: 1.964 / Mean I/σ(I) obs: 14.4 / Num. unique obs: 1900 / CC1/2: 0.525 / Rpim(I) all: 0.539 / Rrim(I) all: 2.038 / % possible all: 59.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→81.43 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.553 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25755 1820 4.8 %RANDOM
Rwork0.22217 ---
obs0.22383 36161 83.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å2-0 Å2
2---0.29 Å20 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.22→81.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 17 137 5668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125644
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165121
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.8227621
X-RAY DIFFRACTIONr_angle_other_deg0.4791.76711806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.236535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41610858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026680
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021356
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_it1.063.3812707
X-RAY DIFFRACTIONr_mcbond_other1.063.3812707
X-RAY DIFFRACTIONr_mcangle_it1.6836.0663382
X-RAY DIFFRACTIONr_mcangle_other1.6836.0663383
X-RAY DIFFRACTIONr_scbond_it1.1713.5982937
X-RAY DIFFRACTIONr_scbond_other1.1313.592926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8646.5294222
X-RAY DIFFRACTIONr_long_range_B_refined3.2932.935755
X-RAY DIFFRACTIONr_long_range_B_other3.28832.925746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.221→2.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 10 -
Rwork0.337 135 -
obs--4.33 %
Refinement TLS params.Method: refined / Origin x: 14.0389 Å / Origin y: -33.4879 Å / Origin z: 18.1012 Å
111213212223313233
T0.0659 Å2-0.0541 Å2-0.0184 Å2-0.1649 Å20.0379 Å2--0.0661 Å2
L1.4913 °2-0.085 °20.6393 °2-1.1807 °2-0.7055 °2--2.301 °2
S-0.103 Å °0.0701 Å °0.2124 Å °-0.0097 Å °-0.1309 Å °-0.2155 Å °-0.2898 Å °0.0876 Å °0.2339 Å °

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