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- PDB-9gar: Siderophore-binding lipoprotein XusB from Barnesiella viscericola -

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Basic information

Entry
Database: PDB / ID: 9gar
TitleSiderophore-binding lipoprotein XusB from Barnesiella viscericola
ComponentsDUF4374 domain-containing protein
KeywordsMETAL TRANSPORT / Outer membrane / lipoprotein / siderophore / iron piracy
Function / homologyProtein of unknown function DUF4374 / Domain of unknown function (DUF4374) / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / DUF4374 domain-containing protein
Function and homology information
Biological speciesBarnesiella viscericola DSM 18177 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSilale, A. / Soo, Y.L. / 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
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4374 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4403
Polymers52,2851
Non-polymers1552
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-15 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.869, 184.869, 82.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein DUF4374 domain-containing protein


Mass: 52285.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-29 were deleted from the expression construct. C-terminal fusion to LEHHHHHH.
Source: (gene. exp.) Barnesiella viscericola DSM 18177 (bacteria)
Gene: BARVI_05925 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0ET74
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, 23-35% PEG 2000 MME

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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 S 16M / Detector: PIXEL / Date: Mar 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.2→58.46 Å / Num. obs: 12010 / % possible obs: 99.9 % / Redundancy: 27.3 % / Biso Wilson estimate: 64.57 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.104 / Net I/σ(I): 6.8
Reflection shellResolution: 3.2→3.43 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2123 / CC1/2: 0.751 / Rpim(I) all: 0.444 / % possible all: 99.3

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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: 3.2→49.33 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7495
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2768 605 5.06 %
Rwork0.2336 11358 -
obs0.2357 11963 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.54 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 9 0 3586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00123678
X-RAY DIFFRACTIONf_angle_d0.38345013
X-RAY DIFFRACTIONf_chiral_restr0.0405542
X-RAY DIFFRACTIONf_plane_restr0.0035654
X-RAY DIFFRACTIONf_dihedral_angle_d10.06251301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.530.3741430.29812762X-RAY DIFFRACTION98.94
3.53-4.040.31791530.26342793X-RAY DIFFRACTION99.56
4.04-5.080.24391480.20312838X-RAY DIFFRACTION99.77
5.09-49.330.23451610.2152965X-RAY DIFFRACTION99.87

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