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- PDB-9if3: Structure of YIUA from Yersinia ruckeri with Iron and DHB-L-Arg-L-Ser -

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Basic information

Entry
Database: PDB / ID: 9if3
TitleStructure of YIUA from Yersinia ruckeri with Iron and DHB-L-Arg-L-Ser
ComponentsPeriplasmic substrate-binding transport protein
KeywordsMETAL BINDING PROTEIN / Ruckerbactin / Yersinia / siderophore
Function / homology: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / : / : / Periplasmic substrate-binding transport protein
Function and homology information
Biological speciesYersinia ruckeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsThompson, S. / Thomsen, E. / Duhme-Klair, A. / Butler, A. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chem.Commun.(Camb.) / Year: 2025
Title: Yersinia ruckeri YRB periplasmic binding protein YiuA selectively recognizes a Fe(III)-mono-catecholate siderophore.
Authors: Thomsen, E. / Thompson, S. / Stow, P.R. / Cukor, M. / Grogan, G. / Duhme-Klair, A.K. / Butler, A.
History
DepositionFeb 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic substrate-binding transport protein
B: Periplasmic substrate-binding transport protein
C: Periplasmic substrate-binding transport protein
D: Periplasmic substrate-binding transport protein
E: Periplasmic substrate-binding transport protein
F: Periplasmic substrate-binding transport protein
G: Periplasmic substrate-binding transport protein
H: Periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,68950
Polymers306,1558
Non-polymers8,53442
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12020 Å2
ΔGint-231 kcal/mol
Surface area101630 Å2
Unit cell
Length a, b, c (Å)80.073, 80.018, 223.696
Angle α, β, γ (deg.)90.00, 89.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Periplasmic substrate-binding transport protein


Mass: 38269.336 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia ruckeri (bacteria) / Gene: CSF007_11785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085U4N5
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-A1I15 / (2~{S})-2-[[(2~{S})-2-[[2,3-bis(oxidanyl)phenyl]carbonylamino]-5-carbamimidamido-pentanoyl]amino]-3-oxidanyl-propanoic acid


Mass: 397.383 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C16H23N5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Lithium Sulfate; 0.1 M HEPES pH 7.5; 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.45→75.56 Å / Num. obs: 103842 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5069 / CC1/2: 0.97 / Rpim(I) all: 0.23

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→75.56 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.994 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.866 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27667 5183 5 %RANDOM
Rwork0.24694 ---
obs0.24845 98619 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.925 Å2
Baniso -1Baniso -2Baniso -3
1--6.79 Å2-0 Å2-0.01 Å2
2--10.71 Å20 Å2
3----3.92 Å2
Refinement stepCycle: 1 / Resolution: 2.45→75.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20889 0 546 453 21888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01221856
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620321
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.81429765
X-RAY DIFFRACTIONr_angle_other_deg0.5311.75446613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85852765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.691589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.738103242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.23341
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2973.62311078
X-RAY DIFFRACTIONr_mcbond_other3.2963.62311078
X-RAY DIFFRACTIONr_mcangle_it5.1446.50713834
X-RAY DIFFRACTIONr_mcangle_other5.1456.50813835
X-RAY DIFFRACTIONr_scbond_it3.2573.78510778
X-RAY DIFFRACTIONr_scbond_other3.2233.77110709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1536.8615829
X-RAY DIFFRACTIONr_long_range_B_refined7.30834.7824761
X-RAY DIFFRACTIONr_long_range_B_other7.30834.7824762
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 425 -
Rwork0.374 7199 -
obs--99.19 %

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