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- PDB-9x2g: Crystal Structure of Extradiol Dioxygenase (Edo4) from Rhizorhabd... -

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Basic information

Entry
Database: PDB / ID: 9x2g
TitleCrystal Structure of Extradiol Dioxygenase (Edo4) from Rhizorhabdus wittichii RW1
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / Extradiol Dioxygenase / Ring cleaving dioxygenase / 2 / 2' / 3-Trihydroxy biphenyl / 3-Trihydroxy diphenylether
Function / homology
Function and homology information


dioxygenase activity / ferrous iron binding
Similarity search - Function
Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
FLUORIDE ION / : / Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesRhizorhabdus wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKayastha, A. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR40141/BTIS/137/16/2021 India
CitationJournal: Arch.Biochem.Biophys. / Year: 2026
Title: Structural and mechanistic insights into Edo4, an extradiol dioxygenase in dioxin degradation.
Authors: Kayastha, A. / Jangid, K. / Verma, S. / Rana, A. / Kumar, P.
History
DepositionOct 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glyoxalase/bleomycin resistance protein/dioxygenase
C: Glyoxalase/bleomycin resistance protein/dioxygenase
A: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,16719
Polymers132,6054
Non-polymers56215
Water16,718928
1
B: Glyoxalase/bleomycin resistance protein/dioxygenase
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

B: Glyoxalase/bleomycin resistance protein/dioxygenase
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

B: Glyoxalase/bleomycin resistance protein/dioxygenase
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

B: Glyoxalase/bleomycin resistance protein/dioxygenase
A: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,53444
Polymers265,2118
Non-polymers1,32336
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area16520 Å2
ΔGint-46 kcal/mol
Surface area85200 Å2
MethodPISA
2
C: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

C: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

C: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

C: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

D: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,13432
Polymers265,2118
Non-polymers92324
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation5_444-x-1/2,y-1/2,-z-11
crystal symmetry operation6_454x-1/2,-y+1/2,-z-11
crystal symmetry operation7_454y-1,x,-z-11
crystal symmetry operation8_554-y,-x,-z-11
Buried area16360 Å2
ΔGint-43 kcal/mol
Surface area84280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.998, 132.998, 181.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

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Components

#1: Protein
Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 33151.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizorhabdus wittichii RW1 (bacteria) / Strain: RW1 / Gene: Swit_3046 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A9J9LFP0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: F
#4: Chemical
ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 928 / 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: 3.03 Å3/Da / Density % sol: 59.47 % / Description: Plate shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG 4000, 20% v/v glycerol, 0.03M halogens,0.1M bicine/Trizma base pH8.5

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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: Dec 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→25.47 Å / Num. obs: 102234 / % possible obs: 99.76 % / Redundancy: 9.4 % / Biso Wilson estimate: 12.69 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1742 / Rpim(I) all: 0.05978 / Rrim(I) all: 0.1848 / Net I/σ(I): 8.78
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 6 % / Rmerge(I) obs: 0.6059 / Mean I/σ(I) obs: 3.47 / Num. unique obs: 10076 / CC1/2: 0.758 / CC star: 0.929 / Rpim(I) all: 0.2584 / Rrim(I) all: 0.6603 / % possible all: 99.99

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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: 2.05→25.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.742 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22386 5013 4.9 %RANDOM
Rwork0.1933 ---
obs0.19481 97110 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.05→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9308 0 24 928 10260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0129563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.64912950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2751183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.441591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.183101481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027426
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_it1.1990.8654747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.021.545925
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.911.0324816
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.9410.514763
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: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 338 -
Rwork0.243 7056 -
obs--99.99 %
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)
10.4027-0.2427-0.11490.8465-0.08460.59310.00920.05030.0061-0.06980.00220.054-0.0496-0.0428-0.01150.0314-0.01-0.01920.0224-0.00620.0557-26.91653.374-37.613
20.4872-0.1808-0.04950.7083-0.04880.7136-0.024-0.0146-0.0062-0.01460.0426-0.0289-0.02350.0232-0.01860.0457-0.0285-0.02010.0593-0.00470.0635-43.16218.677-52.873
30.9211-0.21440.13670.5060.130.62160.0016-0.0528-0.02610.01220.0114-0.0260.03040.0333-0.0130.0081-0.00180.01070.010.00490.0748-12.98239.5421.259
40.3581-0.05190.32291.0307-0.18330.95840.0595-0.088-0.01860.16880.02770.0440.2781-0.3095-0.08720.2191-0.04720.00450.14280.04320.0162-30.02267.059-89.748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 298
2X-RAY DIFFRACTION1B301 - 303
3X-RAY DIFFRACTION2C1 - 298
4X-RAY DIFFRACTION2C301 - 304
5X-RAY DIFFRACTION3A1 - 298
6X-RAY DIFFRACTION3A301 - 306
7X-RAY DIFFRACTION4D2 - 297
8X-RAY DIFFRACTION4D301 - 302

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