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- PDB-9r0q: Paraoxonase-1 in complex with terbium(III) and 2-hydroxyquinoline -

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Basic information

Entry
Database: PDB / ID: 9r0q
TitleParaoxonase-1 in complex with terbium(III) and 2-hydroxyquinoline
ComponentsSerum paraoxonase/arylesterase 1
KeywordsHYDROLASE / ENZYME:INHIBITOR COMPLEX
Function / homology
Function and homology information


response to organophosphorus / quorum-quenching N-acyl-homoserine lactonase / acyl-L-homoserine-lactone lactonohydrolase activity / arylesterase / aryldialkylphosphatase activity / aryldialkylphosphatase / high-density lipoprotein particle / antioxidant activity / arylesterase activity / calcium ion binding
Similarity search - Function
Arylesterase / Paraoxonase1 / : / Arylesterase / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
BROMIDE ION / QUINOLIN-2(1H)-ONE / TERBIUM(III) ION / Serum paraoxonase/arylesterase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSmerkolj, J. / Pavsic, M. / Golicnik, M.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0170 Slovenia
Slovenian Research Agency55728 Slovenia
Slovenian Research AgencyP1-0140 Slovenia
CitationJournal: Dalton Trans / Year: 2025
Title: Intramolecular sensitization and structure of a Tb3+/2-hydroxyquinoline conjugate in the paraoxonase 1 active site
Authors: Smerkolj, J. / Bahun, M. / Poklar Ulrih, N. / Bavec, A. / Pavsic, M. / Golicnik, M.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 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: Serum paraoxonase/arylesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9989
Polymers40,1491
Non-polymers8488
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-39 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.064, 98.064, 138.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum paraoxonase/arylesterase 1 / PON 1 / Aromatic esterase 1 / A-esterase 1 / Serum aryldialkylphosphatase 1


Mass: 40149.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: part of enterokinase cleavage site at N-terminus + Ala (DDDKA), followed by paraoxonase-1
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PON1, PON / Plasmid: pET-32b(+) / Production host: Escherichia coli B (bacteria) / Variant (production host): Rosetta-gami B(DE3)pLysS
References: UniProt: P27170, arylesterase, quorum-quenching N-acyl-homoserine lactonase, aryldialkylphosphatase

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Non-polymers , 5 types, 68 molecules

#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-OCH / QUINOLIN-2(1H)-ONE / 2-OXOQUINOLINE


Mass: 145.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.16 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 6.5
Details: 16% (w/v) PEG 3350, 0.1 M Bis-Tris Propane, pH 6.50, 0.2 M NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.3 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.35→19.82 Å / Num. obs: 28693 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 43.52 Å2 / CC1/2: 1 / Rpim(I) all: 0.051 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.4 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1428 / CC1/2: 0.41 / Rpim(I) all: 1.073

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS20250119data reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.82 Å / SU ML: 0.3336 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 2605 4.87 %
Rwork0.1902 50905 -
obs0.192 28686 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.63 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 28 60 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782772
X-RAY DIFFRACTIONf_angle_d0.90253780
X-RAY DIFFRACTIONf_chiral_restr0.0583423
X-RAY DIFFRACTIONf_plane_restr0.0068486
X-RAY DIFFRACTIONf_dihedral_angle_d16.4952990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.36661600.32222651X-RAY DIFFRACTION99.79
2.4-2.440.35791370.33062673X-RAY DIFFRACTION100
2.44-2.490.31531460.29212681X-RAY DIFFRACTION99.96
2.49-2.550.35091340.28772665X-RAY DIFFRACTION100
2.55-2.610.27451420.27772699X-RAY DIFFRACTION100
2.61-2.670.27491420.26312659X-RAY DIFFRACTION99.89
2.67-2.740.2651400.24572685X-RAY DIFFRACTION100
2.74-2.820.25471240.23042672X-RAY DIFFRACTION100
2.82-2.910.25781300.23422671X-RAY DIFFRACTION100
2.91-3.020.23291370.21122727X-RAY DIFFRACTION100
3.02-3.140.27281490.20072651X-RAY DIFFRACTION99.93
3.14-3.280.23721450.20442667X-RAY DIFFRACTION100
3.28-3.450.26381380.18392670X-RAY DIFFRACTION100
3.45-3.670.21171300.1732672X-RAY DIFFRACTION100
3.67-3.950.21281420.17122711X-RAY DIFFRACTION100
3.95-4.340.16171010.15362690X-RAY DIFFRACTION100
4.34-4.960.17311320.12922684X-RAY DIFFRACTION100
4.96-6.220.20761290.15862701X-RAY DIFFRACTION100
6.22-19.820.19291470.16542676X-RAY DIFFRACTION99.93

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