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- PDB-9hqe: Bacteroides fragilis xenosiderophore-binding lipoprotein XusB -

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Basic information

Entry
Database: PDB / ID: 9hqe
TitleBacteroides fragilis xenosiderophore-binding lipoprotein XusB
ComponentsXusB
KeywordsMETAL TRANSPORT / Bacteroides / lipoprotein / xenosiderophore / iron
Function / homologyProtein of unknown function DUF4374 / Domain of unknown function (DUF4374) / Prokaryotic membrane lipoprotein lipid attachment site profile. / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSilale, 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
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XusB
B: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6688
Polymers90,9702
Non-polymers6986
Water5,909328
1
A: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6352
Polymers45,4851
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0336
Polymers45,4851
Non-polymers5485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.987, 86.925, 154.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein XusB


Mass: 45484.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF9343_4228 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L7E3
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
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 % sol: 34.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M magnesium chloride hexadydrate, 0.1 M HEPES, 22% polyacrylic acid sodium salt 5,100

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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 XE 16M / Detector: PIXEL / Date: Mar 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.77→48.42 Å / Num. obs: 67890 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.2
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 2 / Num. unique obs: 3826 / CC1/2: 0.799 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→48.42 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 3410 5.03 %
Rwork0.1987 64327 -
obs0.2006 67737 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.43 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 45 328 6081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065876
X-RAY DIFFRACTIONf_angle_d0.79337967
X-RAY DIFFRACTIONf_chiral_restr0.0564880
X-RAY DIFFRACTIONf_plane_restr0.00631035
X-RAY DIFFRACTIONf_dihedral_angle_d15.08062095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.30521670.28482639X-RAY DIFFRACTION99.86
1.8-1.820.35581220.26312648X-RAY DIFFRACTION99.78
1.82-1.850.2571250.24642637X-RAY DIFFRACTION99.96
1.85-1.880.25261440.24052664X-RAY DIFFRACTION99.82
1.88-1.910.30681270.25892635X-RAY DIFFRACTION99.64
1.91-1.950.32371380.28322656X-RAY DIFFRACTION99.64
1.95-1.990.32061500.21842625X-RAY DIFFRACTION99.82
1.99-2.030.23091410.20612652X-RAY DIFFRACTION99.96
2.03-2.070.23851370.21812658X-RAY DIFFRACTION99.93
2.07-2.120.23771590.21672651X-RAY DIFFRACTION99.89
2.12-2.170.26721370.2132653X-RAY DIFFRACTION99.96
2.17-2.230.2631330.20712671X-RAY DIFFRACTION100
2.23-2.30.29631310.24392645X-RAY DIFFRACTION99.39
2.3-2.370.26771240.20792677X-RAY DIFFRACTION100
2.37-2.450.22411400.20342684X-RAY DIFFRACTION99.96
2.45-2.550.2311500.20412682X-RAY DIFFRACTION99.96
2.55-2.670.24671540.21062658X-RAY DIFFRACTION100
2.67-2.810.28791490.21882689X-RAY DIFFRACTION99.96
2.81-2.990.2771360.21512692X-RAY DIFFRACTION100
2.99-3.220.24711330.20312708X-RAY DIFFRACTION100
3.22-3.540.19711480.18942695X-RAY DIFFRACTION100
3.54-4.050.21861600.17452729X-RAY DIFFRACTION99.97
4.05-5.10.18181510.14952775X-RAY DIFFRACTION100
5.1-48.420.20991540.17822904X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.516960459310.541946925205-0.0635191806991.0277544512-0.5895953733823.54255504479-0.03124371986860.02367722441780.195038909282-0.01705642559990.0677169787240.0639000019812-0.261070904892-0.33073778281-0.006447895892550.1337810124460.03516737791430.0102022794520.228594850434-0.008973713052510.2506158929240.71229066530162.7826049371111.812787025
21.58459513691-0.2463908537731.50426831110.0451127177274-0.2479882483841.45629491861-0.0529634109656-0.232316811534-0.075618562850.08308695737-0.0104213075120.0909707898291-0.0881039180686-0.3043615594310.06349854818880.181826670314-0.002218137180080.01867259544380.29301785957-0.009715650468960.2683450776691.2176914943151.7960854478119.177738893
34.696978524180.275161999266-0.8084387460084.44710119088-0.9490439740214.48660394373-0.177202923033-0.4753776503510.2812155539810.3408658115940.03393636421990.172912394735-0.329539340106-0.2234092703910.2303994445260.188530640190.05609852509730.007444711128960.2120490526430.003020568669020.2159888649018.6666083490548.0492094396129.014654246
40.552464160427-0.017005513119-0.07032777923951.22151361464-0.4889988660060.8936887500790.002434096192580.00253451558408-0.04346863190780.0942852736525-0.0795303457234-0.259927019549-0.01663636341380.07158984765680.07152533263510.0910422794775-0.010891268017-0.01345776417930.1686867386450.01841474411260.24009323366624.584932806755.0102420535119.197413204
51.94027319611-0.875596685104-0.4148409754922.38882860068-0.4363037716743.39465813074-0.05534806301820.1317235189060.0490197011972-0.0635452623197-0.0222586353464-0.01328232808330.0576770606467-0.01651074335730.02198092101150.094055852254-0.0004462435756-0.0009457478854880.1866673552230.00879852506430.2033599452211.686451842564.533608456102.56467949
60.18137883794-0.1238119319750.06357538360550.284005330978-0.5133882769091.68062009890.06948741153080.0250404874087-0.0559831044075-0.006183939889040.02970390888170.01928553477430.240426556692-0.02593955053130.09766652643191.302331297290.0804330492865-0.06537802262320.3221617466920.05351191620630.299917100812-0.68147424408724.050701598983.3958521534
70.1382640747070.1869504291960.1858519595850.72715379120.2377742660320.5069648164480.0935133832615-0.0456775644871-0.198126783919-0.00827417902010.06657758073120.05844712949570.6834790245210.01840644598380.1828070801921.25914831247-0.106001238942-0.1027971598040.3244601693530.09046975908720.327574489573-5.1129978855828.67297474883.1079209989
80.8115336437290.927800822998-0.8328497364271.06684924409-0.9569159434410.8552679440850.0682670604576-0.197668035983-0.146310188550.1404897568420.07925645622640.3036067705230.73817319905-0.283788256395-0.568023965930.700402467174-0.1620325249670.02554662113350.4241021556770.07753331367160.304675580268-16.486607820437.111076548482.2085909156
90.882167477252-0.1476305248730.1819150658490.9712844337480.09980235968282.663998570110.01525063010980.007517323962450.05504777907950.09302752748550.05021956716920.1504870908020.23534310854-0.33753836711-0.08281260457870.268669409235-0.005575348840210.02124290666160.2389709527530.03158047536420.241312563052-8.441791305352.948846896576.0352743895
100.2134413593280.04257207040090.1625565703290.7630389256760.0549610017441.457399858350.0415238599356-0.00596897817959-0.00145058087570.1773859978870.160485321063-0.03824135275230.7825820217240.550527400573-0.04037624472680.4504091773220.16436898432-0.03852635078280.331222973779-0.05101313864720.2254080085458.7949903688245.784643640281.1033966005
110.271267150635-0.08948380771680.4438876103210.351090605134-0.1619618331440.73048940422-0.0526006376925-0.0620040718194-0.06128381640760.004642405415560.103950666664-0.04353740798210.4666325670740.2467545183220.3031514949571.089755965030.344483345039-0.08340213822450.409390074031-0.006339136183350.2965005835878.2668140956434.185405727188.1254679547
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 103 )AA30 - 1031 - 74
22chain 'A' and (resid 104 through 128 )AA104 - 12875 - 99
33chain 'A' and (resid 129 through 157 )AA129 - 157100 - 127
44chain 'A' and (resid 158 through 364 )AA158 - 364128 - 334
55chain 'A' and (resid 365 through 408 )AA365 - 408335 - 378
66chain 'B' and (resid 31 through 57 )BC31 - 571 - 27
77chain 'B' and (resid 58 through 101 )BC58 - 10128 - 66
88chain 'B' and (resid 102 through 136 )BC102 - 13667 - 95
99chain 'B' and (resid 137 through 305 )BC137 - 30596 - 264
1010chain 'B' and (resid 306 through 364 )BC306 - 364265 - 323
1111chain 'B' and (resid 365 through 406 )BC365 - 406324 - 365

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