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- PDB-9gcz: XusB lipoprotein bound to ferric enterobactin -

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Basic information

Entry
Database: PDB / ID: 9gcz
TitleXusB lipoprotein bound to ferric enterobactin
ComponentsDUF4374 domain-containing protein
KeywordsMETAL BINDING PROTEIN / Lipoprotein / xenosiderophore / iron piracy
Function / homologyProtein of unknown function DUF4374 / Domain of unknown function (DUF4374) / CITRIC ACID / Chem-EB4 / : / DUF4374 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSilale, A. / Mark, H. / Basle, A. / 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
DepositionAug 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 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

Downloads & links

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Assembly

Deposited unit
A: DUF4374 domain-containing protein
B: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,65310
Polymers96,8132
Non-polymers1,8408
Water15,799877
1
A: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4256
Polymers48,4061
Non-polymers1,0195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2284
Polymers48,4061
Non-polymers8213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.992, 48.180, 135.466
Angle α, β, γ (deg.)90.000, 96.787, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DUF4374 domain-containing protein


Mass: 48406.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_2064 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A622

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Non-polymers , 7 types, 885 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin


Mass: 669.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O15 / Feature type: SUBJECT OF INVESTIGATION
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M citric acid, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 1.5→39.17 Å / Num. obs: 122900 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.66 Å2 / CC1/2: 0.774 / Rpim(I) all: 0.096 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5684 / CC1/2: 0.545 / Rpim(I) all: 0.955 / % possible all: 99.4

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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: 1.5→38.05 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9593
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 6022 4.95 %
Rwork0.2038 115635 -
obs0.2057 121657 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 0 121 877 7574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556858
X-RAY DIFFRACTIONf_angle_d0.82489341
X-RAY DIFFRACTIONf_chiral_restr0.05661019
X-RAY DIFFRACTIONf_plane_restr0.0071206
X-RAY DIFFRACTIONf_dihedral_angle_d12.69222388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.50371750.44223209X-RAY DIFFRACTION83.82
1.52-1.530.51861890.48153443X-RAY DIFFRACTION88.41
1.53-1.550.34771740.33353827X-RAY DIFFRACTION97.23
1.55-1.570.28961930.2763858X-RAY DIFFRACTION99.83
1.57-1.590.29872100.26123869X-RAY DIFFRACTION99.73
1.59-1.620.26241930.25193892X-RAY DIFFRACTION99.83
1.62-1.640.30021980.24773854X-RAY DIFFRACTION99.7
1.64-1.660.30942070.23983938X-RAY DIFFRACTION99.93
1.66-1.690.27892060.23133798X-RAY DIFFRACTION99.9
1.69-1.720.30032110.26933948X-RAY DIFFRACTION99.33
1.72-1.750.32262050.25113802X-RAY DIFFRACTION99.13
1.75-1.780.25182200.20443881X-RAY DIFFRACTION99.9
1.78-1.810.24271980.19783838X-RAY DIFFRACTION99.85
1.81-1.850.25631920.20253924X-RAY DIFFRACTION99.88
1.85-1.890.33732080.25763870X-RAY DIFFRACTION99.2
1.89-1.930.33992090.29593811X-RAY DIFFRACTION97.31
1.93-1.980.24651960.21873859X-RAY DIFFRACTION99.66
1.98-2.040.22371810.19023900X-RAY DIFFRACTION99.85
2.04-2.10.32041840.23143859X-RAY DIFFRACTION97.68
2.1-2.160.21232210.18773851X-RAY DIFFRACTION99.95
2.16-2.240.25822290.19363876X-RAY DIFFRACTION99.59
2.24-2.330.23312090.19713906X-RAY DIFFRACTION99.16
2.33-2.440.20982220.17443871X-RAY DIFFRACTION99.95
2.44-2.560.20771840.18613966X-RAY DIFFRACTION99.98
2.56-2.730.24391980.19833897X-RAY DIFFRACTION99.42
2.73-2.940.22852010.19513932X-RAY DIFFRACTION100
2.94-3.230.23711870.18483968X-RAY DIFFRACTION100
3.23-3.70.20172040.16023939X-RAY DIFFRACTION99.33
3.7-4.660.15721850.14093977X-RAY DIFFRACTION99.52
4.66-38.050.19762330.17954072X-RAY DIFFRACTION99.79

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