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- PDB-9ht5: Structure of YIUA from Yersinia ruckeri with Iron and nitrilotria... -

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Basic information

Entry
Database: PDB / ID: 9ht5
TitleStructure of YIUA from Yersinia ruckeri with Iron and nitrilotriacetic acid
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. / : / NITRILOTRIACETIC ACID / 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 with Iron and nitrilotriacetic acid
Authors: Thompson, S. / Thomsen, E. / Duhme-Klair, A. / Butler, A. / Grogan, G.
History
DepositionDec 19, 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
C: Periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8589
Polymers114,1173
Non-polymers7416
Water4,288238
1
A: Periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2863
Polymers38,0391
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2863
Polymers38,0391
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic substrate-binding transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2863
Polymers38,0391
Non-polymers2472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.146, 59.386, 101.171
Angle α, β, γ (deg.)101.36, 94.49, 100.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Periplasmic substrate-binding transport protein


Mass: 38039.055 Da / Num. of mol.: 3
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-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% (w/v) PEG 1000; 12.5% (w/v) PEG 3350; 12.5% (v/v) MPD; 0.02 M alcohols; 0.1 M MES/imidazole pH 6.5 (Molecular Dimensions Morpheus D4)

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.77296 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77296 Å / Relative weight: 1
ReflectionResolution: 2.14→54.78 Å / Num. obs: 47589 / % possible obs: 98.9 % / Redundancy: 3.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.17 / Net I/σ(I): 4.4
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3904 / CC1/2: 0.57 / Rpim(I) all: 0.96

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→54.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.848 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25343 2329 4.9 %RANDOM
Rwork0.20501 ---
obs0.20728 45243 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.65 Å21.98 Å2
2---2.98 Å20.12 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.14→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7497 0 42 238 7777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167166
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.78910506
X-RAY DIFFRACTIONr_angle_other_deg0.571.72916431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.495998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.136531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.752101119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021755
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_it3.1923.4034010
X-RAY DIFFRACTIONr_mcbond_other3.1893.4014007
X-RAY DIFFRACTIONr_mcangle_it4.6696.0994996
X-RAY DIFFRACTIONr_mcangle_other4.6666.0984995
X-RAY DIFFRACTIONr_scbond_it3.4823.5433699
X-RAY DIFFRACTIONr_scbond_other3.4833.5433695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2926.4415509
X-RAY DIFFRACTIONr_long_range_B_refined7.02934.898761
X-RAY DIFFRACTIONr_long_range_B_other7.0334.668744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 196 -
Rwork0.305 3348 -
obs--98.25 %

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