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- PDB-9gar: Siderophore-binding lipoprotein XusB from Barnesiella viscericola -

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Basic information

Entry
Database: PDB / ID: 9gar
TitleSiderophore-binding lipoprotein XusB from Barnesiella viscericola
ComponentsDUF4374 domain-containing protein
KeywordsMETAL TRANSPORT / Outer membrane / lipoprotein / siderophore / iron piracy
Function / homologyProtein of unknown function DUF4374 / Domain of unknown function (DUF4374) / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / DUF4374 domain-containing protein
Function and homology information
Biological speciesBarnesiella viscericola DSM 18177 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSilale, A. / Soo, Y.L. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Structural basis of iron piracy by human gut .
Authors: Augustinas Silale / Yung Li Soo / Hannah Mark / Rachel N Motz / Arnaud Baslé / Elizabeth M Nolan / Bert van den Berg /
Abstract: Iron is an essential element that can be growth-limiting in microbial communities, particularly those present within host organisms. To acquire iron, many bacteria secrete siderophores, secondary ...Iron is an essential element that can be growth-limiting in microbial communities, particularly those present within host organisms. To acquire iron, many bacteria secrete siderophores, secondary metabolites that chelate ferric iron. These iron chelates can be transported back into the cell via TonB-dependent transporters in the outer membrane, followed by intracellular liberation of the iron. Pathogenic and produce siderophores during gut infection. In response to iron starvation, the human gut symbiont upregulates an iron piracy system, XusABC, which steals iron-bound siderophores from the invading pathogens. Here, we investigated the molecular details of xenosiderophore uptake across the outer membrane by the XusAB complex. Our crystal and cryogenic electron microscopy structures explain how the XusB lipoprotein recognises iron-bound xenosiderophores and passes them on to the XusA TonB-dependent transporter. Moreover, we show that Xus homologues can transport a variety of siderophores with different iron-chelating functional groups.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4403
Polymers52,2851
Non-polymers1552
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-15 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.869, 184.869, 82.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein DUF4374 domain-containing protein


Mass: 52285.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-29 were deleted from the expression construct. C-terminal fusion to LEHHHHHH.
Source: (gene. exp.) Barnesiella viscericola DSM 18177 (bacteria)
Gene: BARVI_05925 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0ET74
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
Has ligand of interestN
Has protein modificationN

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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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 23-35% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→58.46 Å / Num. obs: 12010 / % possible obs: 99.9 % / Redundancy: 27.3 % / Biso Wilson estimate: 64.57 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.104 / Net I/σ(I): 6.8
Reflection shellResolution: 3.2→3.43 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2123 / CC1/2: 0.751 / Rpim(I) all: 0.444 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
Aimlessdata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.33 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2768 605 5.06 %
Rwork0.2336 11358 -
obs0.2357 11963 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.54 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 9 0 3586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00123678
X-RAY DIFFRACTIONf_angle_d0.38345013
X-RAY DIFFRACTIONf_chiral_restr0.0405542
X-RAY DIFFRACTIONf_plane_restr0.0035654
X-RAY DIFFRACTIONf_dihedral_angle_d10.06251301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.530.3741430.29812762X-RAY DIFFRACTION98.94
3.53-4.040.31791530.26342793X-RAY DIFFRACTION99.56
4.04-5.080.24391480.20312838X-RAY DIFFRACTION99.77
5.09-49.330.23451610.2152965X-RAY DIFFRACTION99.87

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