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- PDB-9hqk: Bacteroides fragilis lipoprotein XusB bound to ferrichrome -

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Basic information

Entry
Database: PDB / ID: 9hqk
TitleBacteroides fragilis lipoprotein XusB bound to ferrichrome
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. / FERRICHROME / : / Uncharacterized protein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsSilale, A. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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

Downloads & links

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Assembly

Deposited unit
A: XusB
B: XusB
C: XusB
D: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,12512
Polymers181,9394
Non-polymers3,1858
Water00
1
A: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2813
Polymers45,4851
Non-polymers7962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2813
Polymers45,4851
Non-polymers7962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2813
Polymers45,4851
Non-polymers7962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: XusB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2813
Polymers45,4851
Non-polymers7962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.195, 155.972, 89.624
Angle α, β, γ (deg.)90.000, 95.563, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 32 through 405 or (resid 406...
d_2ens_1(chain "B" and (resid 32 through 406 or resid 501))
d_3ens_1(chain "C" and (resid 32 through 405 or (resid 406...
d_4ens_1(chain "D" and (resid 32 through 406 or resid 501))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUASPASPAA32 - 40632 - 406
d_12FCEFCEFCEFCEAE501
d_21GLUGLUASPASPBB32 - 40632 - 406
d_22FCEFCEFCEFCEBG501
d_31GLUGLUASPASPCC32 - 40632 - 406
d_32FCEFCEFCEFCECI501
d_41GLUGLUASPASPDD32 - 40632 - 406
d_42FCEFCEFCEFCEDK501

NCS oper:
IDCodeMatrixVector
1given(-0.9944020369023, -0.07236593746518, -0.076991948276006), (0.070659432426175, -0.99719547787457, 0.024666242431921), (-0.078561018410916, 0.01908795435046, 0.99672655045652)24.074834795432, 0.18390532462713, 45.611457074647
2given(0.53320819761233, 0.71864242775463, 0.4463654097597), (-0.37519763967767, 0.67378290810941, -0.63658724768874), (-0.75823198902401, 0.17195829078751, 0.62889951268078)-0.18554151459915, 54.840727626659, 41.42492776626
3given(0.62323683228626, 0.64180177230231, 0.4468403920321), (0.30571003326701, -0.72586197828159, 0.61617023949962), (0.71980360268734, -0.24741639710164, -0.64858916118262)29.263291407194, 25.203578025167, 3.2365182567301

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Components

#1: Protein
XusB


Mass: 45484.863 Da / Num. of mol.: 4
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-FCE / FERRICHROME


Mass: 740.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H42FeN9O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES 7.5, 22 % w/v Poly(acrylic acid sodium salt) 5100

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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: Apr 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.32→58.71 Å / Num. obs: 23146 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.9 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.116 / Net I/σ(I): 5.3
Reflection shellResolution: 3.32→3.59 Å / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4780 / CC1/2: 0.862 / Rpim(I) all: 0.318 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXv1.21refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→58.71 Å / SU ML: 0.4649 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.4077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2962 1140 4.97 %
Rwork0.2485 21791 -
obs0.2509 22931 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.06 Å2
Refinement stepCycle: LAST / Resolution: 3.32→58.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11616 0 196 0 11812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002512083
X-RAY DIFFRACTIONf_angle_d0.630216423
X-RAY DIFFRACTIONf_chiral_restr0.0471795
X-RAY DIFFRACTIONf_plane_restr0.0052150
X-RAY DIFFRACTIONf_dihedral_angle_d13.78764309
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.44380047943334
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.60183920486477
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.61008788151413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.470.36691480.33732706X-RAY DIFFRACTION99.37
3.47-3.650.3991480.32882711X-RAY DIFFRACTION99.34
3.65-3.880.34621490.30562724X-RAY DIFFRACTION99.52
3.88-4.180.31711390.27032685X-RAY DIFFRACTION98.43
4.18-4.60.29051490.23282720X-RAY DIFFRACTION99.03
4.6-5.270.25411410.21772723X-RAY DIFFRACTION98.86
5.27-6.640.25191410.22672726X-RAY DIFFRACTION99.27
6.64-58.710.23081250.17882796X-RAY DIFFRACTION99.29

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