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

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Basic information

Entry
Database: PDB / ID: 8rmi
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 / Metal-pseudopaline receptor CntO
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsJosts, I. / Tidow, H. / Mislin, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Bioorg.Med.Chem. / Year: 2024
Title: Synthesis and antibacterial properties under blue LED light of conjugates between the siderophore desferrioxamine B (DFOB) and an Iridium(III) complex.
Authors: Faucon, A. / Renault, J. / Josts, I. / Couchot, J. / Renaud, J.L. / Hoegy, F. / Plesiat, P. / Tidow, H. / Gaillard, S. / Mislin, G.L.A.
History
DepositionJan 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 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)92,48114
Polymers90,0581
Non-polymers2,42213
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-89 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.515, 93.515, 177.817
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, 3 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 50 molecules

#3: Chemical ChemComp-A1H1Z / [1-[2-[2-[2-[2-[2-(dipyridin-2-ylamino)ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]methyl ~{N}-[5-[[4-[5-[[4-[5-[ethanoyl(oxidanyl)amino]pentylamino]-4-oxidanylidene-butanoyl]-oxidanyl-amino]pentylamino]-4-oxidanylidene-butanoyl]-oxidanyl-amino]pentyl]carbamate


Mass: 1072.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H77N13O14 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.48→80.99 Å / Num. obs: 16422 / % possible obs: 93.6 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.04 / Rrim(I) all: 0.153 / Net I/σ(I): 13.1
Reflection shellResolution: 2.48→2.85 Å / Rmerge(I) obs: 1.546 / Num. unique obs: 820 / CC1/2: 0.851 / Rpim(I) all: 0.399 / Rrim(I) all: 1.598

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→80.99 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU B: 18.531 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26818 845 5.1 %RANDOM
Rwork0.2187 ---
obs0.22119 15576 50.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å2-0 Å2
3----2.33 Å2
Refinement stepCycle: 1 / Resolution: 2.48→80.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 155 39 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125599
X-RAY DIFFRACTIONr_bond_other_d0.0050.0165012
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.8257585
X-RAY DIFFRACTIONr_angle_other_deg0.9361.77911547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2335676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.02535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07610858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026691
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021357
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_it4.0174.5962707
X-RAY DIFFRACTIONr_mcbond_other4.0174.5962707
X-RAY DIFFRACTIONr_mcangle_it6.3148.2593382
X-RAY DIFFRACTIONr_mcangle_other6.3138.2593383
X-RAY DIFFRACTIONr_scbond_it5.345.252892
X-RAY DIFFRACTIONr_scbond_other5.145.2012869
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0329.3344168
X-RAY DIFFRACTIONr_long_range_B_refined13.74107.8383582
X-RAY DIFFRACTIONr_long_range_B_other13.741107.8383583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.482→2.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.75 3 -
Rwork0.305 50 -
obs--2.25 %
Refinement TLS params.Method: refined / Origin x: 13.917 Å / Origin y: -32.8802 Å / Origin z: 17.802 Å
111213212223313233
T0.0781 Å2-0.016 Å2-0.04 Å2-0.0264 Å20.0354 Å2--0.0771 Å2
L1.6086 °2-0.0142 °20.4389 °2-1.0564 °2-0.6161 °2--1.8304 °2
S-0.152 Å °0.118 Å °0.2769 Å °-0.0296 Å °-0.1058 Å °-0.158 Å °-0.3083 Å °0.1083 Å °0.2577 Å °

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