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- PDB-9gcy: Xenosiderophore-binding lipoprotein XusB from Bacteroides thetaio... -

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Basic information

Entry
Database: PDB / ID: 9gcy
TitleXenosiderophore-binding lipoprotein XusB from Bacteroides thetaiotaomicron
ComponentsDUF4374 domain-containing protein
KeywordsMETAL TRANSPORT / Outer membrane / lipoprotein / iron piracy
Function / homologyProtein of unknown function DUF4374 / Domain of unknown function (DUF4374) / DUF4374 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSilale, A. / Mark, H. / van den Berg, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214222/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: Structural basis of iron piracy by human gut Bacteroides
Authors: Silale, A. / Soo, Y.L. / Mark, H. / Basle, A. / van den Berg, B.
History
DepositionAug 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 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: DUF4374 domain-containing protein
B: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3548
Polymers96,8132
Non-polymers5426
Water20,6631147
1
A: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6373
Polymers48,4061
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7175
Polymers48,4061
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.705, 108.633, 93.894
Angle α, β, γ (deg.)90.000, 96.574, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1147 / 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 Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M calcium chloride, 0.1M MES pH 6.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.56→54.32 Å / Num. obs: 129093 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.35 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.039 / Net I/σ(I): 11
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6316 / CC1/2: 0.621 / Rpim(I) all: 0.652 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→46.94 Å / SU ML: 0.1889 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 6471 5.02 %
Rwork0.1757 122459 -
obs0.1773 128930 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 1.56→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 0 28 1147 7692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046733
X-RAY DIFFRACTIONf_angle_d0.99379176
X-RAY DIFFRACTIONf_chiral_restr0.07121018
X-RAY DIFFRACTIONf_plane_restr0.00911178
X-RAY DIFFRACTIONf_dihedral_angle_d12.13492392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.32782140.30144066X-RAY DIFFRACTION98.98
1.58-1.60.28812160.25653987X-RAY DIFFRACTION99.81
1.6-1.620.26482200.2494065X-RAY DIFFRACTION99.84
1.62-1.640.27372120.23934112X-RAY DIFFRACTION99.82
1.64-1.660.29041820.22294054X-RAY DIFFRACTION99.74
1.66-1.680.24842630.21954038X-RAY DIFFRACTION99.88
1.68-1.70.25522130.21954064X-RAY DIFFRACTION99.79
1.7-1.730.27362370.21164065X-RAY DIFFRACTION99.65
1.73-1.760.25962070.20854091X-RAY DIFFRACTION99.95
1.76-1.790.25352220.20594061X-RAY DIFFRACTION99.93
1.79-1.820.24352450.20644037X-RAY DIFFRACTION99.86
1.82-1.850.2612030.21264071X-RAY DIFFRACTION99.88
1.85-1.890.25462050.20584065X-RAY DIFFRACTION99.86
1.89-1.920.23952110.20994097X-RAY DIFFRACTION99.77
1.92-1.970.24782140.19864073X-RAY DIFFRACTION99.81
1.97-2.010.22372440.19044041X-RAY DIFFRACTION99.98
2.01-2.060.22222080.18464099X-RAY DIFFRACTION99.98
2.06-2.120.22812150.18724057X-RAY DIFFRACTION99.93
2.12-2.180.20682140.17484136X-RAY DIFFRACTION99.93
2.18-2.250.22442140.18174049X-RAY DIFFRACTION99.95
2.25-2.330.24312090.1794080X-RAY DIFFRACTION99.95
2.33-2.420.23121850.17924148X-RAY DIFFRACTION99.98
2.42-2.530.21832030.17974121X-RAY DIFFRACTION100
2.53-2.670.19922120.17444073X-RAY DIFFRACTION100
2.67-2.830.21131880.18114132X-RAY DIFFRACTION100
2.83-3.050.22092310.17324090X-RAY DIFFRACTION100
3.05-3.360.18652410.16524063X-RAY DIFFRACTION100
3.36-3.850.16612140.15234118X-RAY DIFFRACTION99.98
3.85-4.850.14072190.13014108X-RAY DIFFRACTION100
4.85-46.940.17412100.15594198X-RAY DIFFRACTION99.84

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