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- PDB-9ioy: Isophthalate dioxygenase in complex with isophthalate -

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Basic information

Entry
Database: PDB / ID: 9ioy
TitleIsophthalate dioxygenase in complex with isophthalate
ComponentsRieske (2Fe-2S) domain protein
KeywordsOXIDOREDUCTASE / Rieske oxygenase / non-heme iron / Rieske center / mononuclear iron
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
LigXa-like, C-terminal domain / LigXa C-terminal domain like / : / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
benzene-1,3-dicarboxylic acid / : / FE2/S2 (INORGANIC) CLUSTER / Rieske (2Fe-2S) domain protein
Similarity search - Component
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJangid, K. / Mahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J.Bacteriol. / Year: 2025
Title: Structure-guided engineering of an aromatic ring-hydroxylating dioxygenase for broad-spectrum phthalate degradation.
Authors: Mahto, J.K. / Mishra, I. / Jangid, K. / Kumar, P.
History
DepositionJul 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 1, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rieske (2Fe-2S) domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1244
Polymers50,7261
Non-polymers3983
Water00
1
A: Rieske (2Fe-2S) domain protein
hetero molecules

A: Rieske (2Fe-2S) domain protein
hetero molecules

A: Rieske (2Fe-2S) domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,37112
Polymers152,1783
Non-polymers1,1939
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area9120 Å2
ΔGint-115 kcal/mol
Surface area45750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.956, 146.956, 146.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Rieske (2Fe-2S) domain protein / isophthalate dioxygenase


Mass: 50725.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni KF-1 (bacteria) / Gene: CtesDRAFT_PD2139 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WRK8
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-8G0 / benzene-1,3-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 5.29 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium fluoride 0.2 M, PEG 3350 20%, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→25.22 Å / Num. obs: 15945 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.965 / Net I/σ(I): 9.9
Reflection shellResolution: 3.3→3.57 Å / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 10174

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→25.22 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.06 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.924 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21764 772 4.8 %RANDOM
Rwork0.17456 ---
obs0.17652 15342 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.196 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.3→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 17 0 3484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123583
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163231
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.8324861
X-RAY DIFFRACTIONr_angle_other_deg0.6471.7627457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9895434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.218529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95910573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
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_it6.5866.4481739
X-RAY DIFFRACTIONr_mcbond_other6.5786.4491739
X-RAY DIFFRACTIONr_mcangle_it10.25611.5852172
X-RAY DIFFRACTIONr_mcangle_other10.25611.5852173
X-RAY DIFFRACTIONr_scbond_it7.5196.9611844
X-RAY DIFFRACTIONr_scbond_other7.5176.961845
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.67112.5572686
X-RAY DIFFRACTIONr_long_range_B_refined14.5169.864119
X-RAY DIFFRACTIONr_long_range_B_other14.50969.864120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.302→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 56 -
Rwork0.188 1104 -
obs--99.91 %

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