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- PDB-9vdb: Crystal Structure of Dioxin Dioxygenase from Rhizorhabdus wittich... -

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Basic information

Entry
Database: PDB / ID: 9vdb
TitleCrystal Structure of Dioxin Dioxygenase from Rhizorhabdus wittichii RW1
Components
  • Aromatic-ring-hydroxylating dioxygenase, beta subunit
  • Ring hydroxylating dioxygenase, alpha subunit
KeywordsOXIDOREDUCTASE / Dioxygenase / dibenzo-p-dioxin / dibenzofuran / Rieske oxygenase
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 dioxygenase, alpha subunit NdoB-like, C-terminal / 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) / 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 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / 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) / 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 / NTF2-like domain superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / Aromatic-ring-hydroxylating dioxygenase, beta subunit / Ring hydroxylating dioxygenase, alpha subunit
Similarity search - Component
Biological speciesRhizorhabdus wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKayastha, A. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR40141/BTIS/137/16/2021 India
CitationJournal: To Be Published
Title: Crystal Structure of Dioxin Dioxygenase from Rhizorhabdus wittichii RW1
Authors: Kayastha, A. / Kumar, P.
History
DepositionJun 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 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: Ring hydroxylating dioxygenase, alpha subunit
B: Aromatic-ring-hydroxylating dioxygenase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64017
Polymers69,5042
Non-polymers1,13615
Water1,53185
1
A: Ring hydroxylating dioxygenase, alpha subunit
B: Aromatic-ring-hydroxylating dioxygenase, beta subunit
hetero molecules

A: Ring hydroxylating dioxygenase, alpha subunit
B: Aromatic-ring-hydroxylating dioxygenase, beta subunit
hetero molecules

A: Ring hydroxylating dioxygenase, alpha subunit
B: Aromatic-ring-hydroxylating dioxygenase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,91951
Polymers208,5126
Non-polymers3,40745
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area35900 Å2
ΔGint-128 kcal/mol
Surface area57950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.572, 137.572, 137.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

21B-319-

HOH

31B-325-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ring hydroxylating dioxygenase, alpha subunit


Mass: 48536.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria) / Strain: RW1 / Gene: Swit_4897 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: A0A9J9HH21
#2: Protein Aromatic-ring-hydroxylating dioxygenase, beta subunit


Mass: 20967.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria) / Strain: RW1 / Gene: Swit_4896 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: A0A9J9HH04

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Non-polymers , 7 types, 100 molecules

#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: 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
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG8000, 0.1M Calcium acetate hydrate, and 0.15 M Sodium cacodylate pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→23.96 Å / Num. obs: 23912 / % possible obs: 98.57 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.33 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1085 / Rpim(I) all: 0.04447 / Rrim(I) all: 0.1175 / Net I/σ(I): 20.23
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.4771 / Mean I/σ(I) obs: 2.94 / Num. unique obs: 2346 / CC1/2: 0.968 / CC star: 0.992 / Rpim(I) all: 0.2184 / Rrim(I) all: 0.5261 / % possible all: 99.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 35.753 / SU ML: 0.324 / Cross valid method: FREE R-VALUE / ESU R: 0.827 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29725 1152 4.8 %RANDOM
Rwork0.23157 ---
obs0.23475 22619 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.472 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.7→23.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 61 85 4921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.6576697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.255596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.808545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78810763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023860
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1221.562390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8652.8042984
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9821.7512565
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.82117.637252
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 84 -
Rwork0.352 1626 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31990.00390.19310.22710.00850.16230.05580.27010.08130.1776-0.01650.08920.13890.24-0.03930.38520.37960.1190.56590.13060.1528-2.708-39.117-33.656
20.54280.22140.29340.20640.02810.34240.04890.14810.09240.0841-0.03210.10170.13710.1752-0.01680.39290.26150.1680.38880.15530.2009-29.694-51.899-43.483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 432
2X-RAY DIFFRACTION1A501 - 508
3X-RAY DIFFRACTION2B9 - 179
4X-RAY DIFFRACTION2B201 - 206

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