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- PDB-9hrj: Structure of YIUA from Yersinia ruckeri -

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Basic information

Entry
Database: PDB / ID: 9hrj
TitleStructure of YIUA from Yersinia ruckeri
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: 2.14 Å
AuthorsThompson, S. / Thomsen, E. / Duhme-Klair, A. / Butler, A. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of YIUA from Yersinia ruckeri
Authors: Thompson, S. / Thomsen, E. / Duhme-Klair, A. / Butler, A. / Grogan, G.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 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


Theoretical massNumber of molelcules
Total (without water)76,5392
Polymers76,5392
Non-polymers00
Water5,242291
1
A: Periplasmic substrate-binding transport protein


Theoretical massNumber of molelcules
Total (without water)38,2691
Polymers38,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic substrate-binding transport protein


Theoretical massNumber of molelcules
Total (without water)38,2691
Polymers38,2691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.598, 68.474, 112.908
Angle α, β, γ (deg.)90.00, 96.75, 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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 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: Jul 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.14→112.16 Å / Num. obs: 16162 / % possible obs: 86.1 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.16 / Net I/σ(I): 5.7
Reflection shellResolution: 2.14→2.57 Å / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 808 / CC1/2: 0.57 / Rpim(I) all: 0.64 / % possible all: 53.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→112.13 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.779 / SU B: 12.04 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3097 768 4.8 %RANDOM
Rwork0.2076 ---
obs0.21233 15393 45.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.067 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.39 Å2
2---0.28 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.14→112.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5125 0 0 291 5416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164978
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.7967099
X-RAY DIFFRACTIONr_angle_other_deg0.4311.74511432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.531524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66510830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021195
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_it1.3212.3742676
X-RAY DIFFRACTIONr_mcbond_other1.3212.3742676
X-RAY DIFFRACTIONr_mcangle_it2.3054.2583335
X-RAY DIFFRACTIONr_mcangle_other2.3054.2593336
X-RAY DIFFRACTIONr_scbond_it1.2552.3982549
X-RAY DIFFRACTIONr_scbond_other1.2552.3982550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1994.3843764
X-RAY DIFFRACTIONr_long_range_B_refined4.91324.686401
X-RAY DIFFRACTIONr_long_range_B_other4.87224.646375
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.144→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.084 0 -
Rwork0.35 12 -
obs--0.46 %

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