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- PDB-9o71: Hexameric Rieske non-heme iron dioxygenase -

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Basic information

Entry
Database: PDB / ID: 9o71
TitleHexameric Rieske non-heme iron dioxygenase
Components
  • Aromatic-ring-hydroxylating dioxygenase beta subunit
  • Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit
KeywordsMETAL BINDING PROTEIN / DIOXYGENASE / HETEROHEXAMER / AROMATIC COMPOUND DEGRADATION
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit / Aromatic-ring-hydroxylating dioxygenase beta subunit
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsJiang, T. / Kozlowski, M.J. / Jeffrey, P.D. / Conway, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Complete characterization of the indole-3-acetic acid (IAA) degradation pathway in Variovorax and expanding its application to root-associated bacteria
Authors: Jiang, T. / Shen, Y. / Li, X. / Kozlowski, M.J. / Jeffrey, P.D. / Groves, J.T. / Rabinowitz, J.D. / Conway, J.M.
History
DepositionApr 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6135
Polymers70,3192
Non-polymers2943
Water13,998777
1
A: Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules

A: Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,83915
Polymers210,9586
Non-polymers8819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area25040 Å2
ΔGint-175 kcal/mol
Surface area64580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.483, 130.483, 101.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

21B-547-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Phenylpropionate dioxygenase-like ring-hydroxylating dioxygenase large terminal subunit


Mass: 51366.828 Da / Num. of mol.: 1 / Mutation: S94N, D165G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: J2W39_005219 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAW8EQ13
#2: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 18952.352 Da / Num. of mol.: 1 / Mutation: T97Q,A106V,V107L,Q135R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP7

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Non-polymers , 4 types, 780 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, sodium citrate tribasic dihydrate (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.28→33.78 Å / Num. obs: 165805 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Χ2: 0.83 / Net I/σ(I): 11.8 / Num. measured all: 1138515
Reflection shellResolution: 1.28→1.35 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.52 / Num. measured all: 165371 / Num. unique obs: 24236 / CC1/2: 0.543 / Rpim(I) all: 0.623 / Rrim(I) all: 1.644 / Χ2: 0.71 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→33.78 Å / SU ML: 0.1312 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.6937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1693 8305 5.01 %
Rwork0.1516 157493 -
obs0.1525 165798 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.78 Å2
Refinement stepCycle: LAST / Resolution: 1.28→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 9 777 5568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865140
X-RAY DIFFRACTIONf_angle_d1.11947008
X-RAY DIFFRACTIONf_chiral_restr0.0817736
X-RAY DIFFRACTIONf_plane_restr0.0076934
X-RAY DIFFRACTIONf_dihedral_angle_d20.74661961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.31272730.29935229X-RAY DIFFRACTION100
1.29-1.310.31942600.29115326X-RAY DIFFRACTION100
1.31-1.330.28752720.26925178X-RAY DIFFRACTION100
1.33-1.340.26742760.26025266X-RAY DIFFRACTION100
1.34-1.360.29572630.2525259X-RAY DIFFRACTION100
1.36-1.380.24162900.24595268X-RAY DIFFRACTION100
1.38-1.40.23482760.23745241X-RAY DIFFRACTION100
1.4-1.420.22222900.22355232X-RAY DIFFRACTION100
1.42-1.440.23242820.21195224X-RAY DIFFRACTION100
1.44-1.470.23082710.20575293X-RAY DIFFRACTION100
1.47-1.490.21482620.19945225X-RAY DIFFRACTION99.98
1.49-1.520.20642630.18325292X-RAY DIFFRACTION100
1.52-1.550.19412480.17315267X-RAY DIFFRACTION100
1.55-1.580.19212880.16755239X-RAY DIFFRACTION100
1.58-1.610.16962930.15645221X-RAY DIFFRACTION100
1.61-1.650.17973220.15475269X-RAY DIFFRACTION100
1.65-1.690.16792690.14835180X-RAY DIFFRACTION100
1.69-1.740.15373180.14295233X-RAY DIFFRACTION99.98
1.74-1.790.15812500.1435275X-RAY DIFFRACTION100
1.79-1.850.16622870.13995239X-RAY DIFFRACTION100
1.85-1.910.15532850.14135271X-RAY DIFFRACTION100
1.91-1.990.16112500.14195256X-RAY DIFFRACTION99.95
1.99-2.080.14713000.13785222X-RAY DIFFRACTION99.98
2.08-2.190.13952870.13575254X-RAY DIFFRACTION100
2.19-2.330.1482680.13635231X-RAY DIFFRACTION100
2.33-2.50.16142590.13395323X-RAY DIFFRACTION100
2.51-2.760.14972740.14035251X-RAY DIFFRACTION100
2.76-3.160.18312780.14365226X-RAY DIFFRACTION100
3.16-3.970.14832840.12995238X-RAY DIFFRACTION99.96
3.98-33.780.15142670.13555265X-RAY DIFFRACTION99.89

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