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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: 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)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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