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- PDB-9ina: Crystal Structure of isophthalate dioxygenase from Comamonas test... -

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Basic information

Entry
Database: PDB / ID: 9ina
TitleCrystal Structure of isophthalate dioxygenase from Comamonas testosteroni KF1
ComponentsRieske (2Fe-2S) domain protein
KeywordsOXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain
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
: / FE2/S2 (INORGANIC) CLUSTER / Rieske (2Fe-2S) domain protein
Similarity search - Component
Biological speciesComamonas testosteroni KF-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsMahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/NBA/37/01/2015 (VIII) 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 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,9583
Polymers50,7261
Non-polymers2322
Water1267
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)152,8739
Polymers152,1783
Non-polymers6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area9320 Å2
ΔGint-111 kcal/mol
Surface area49680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.740, 150.740, 150.740
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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 5.68 Å3/Da / Density % sol: 78.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M potassium thiocyanate, 0.1 M tris-HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→106.82 Å / Num. obs: 23991 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 15
Reflection shellResolution: 2.96→3.14 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3849 / CC1/2: 0.809

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→106.82 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.812 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20571 1206 5 %RANDOM
Rwork0.17484 ---
obs0.1764 22785 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.384 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.96→106.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 5 7 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163260
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.8324929
X-RAY DIFFRACTIONr_angle_other_deg0.6751.7647527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3465440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.763527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06710581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02873
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_it5.9357.4451763
X-RAY DIFFRACTIONr_mcbond_other5.917.4461763
X-RAY DIFFRACTIONr_mcangle_it8.02713.4112202
X-RAY DIFFRACTIONr_mcangle_other8.02613.4142203
X-RAY DIFFRACTIONr_scbond_it7.9048.0981869
X-RAY DIFFRACTIONr_scbond_other7.9138.1031866
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.03414.5432724
X-RAY DIFFRACTIONr_long_range_B_refined12.04473.433890
X-RAY DIFFRACTIONr_long_range_B_other12.04873.433891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.964→3.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 91 -
Rwork0.287 1679 -
obs--100 %

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