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- PDB-23al: Crystal Structure of Extradiol Dioxygenase (Edo4) in complex with... -

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Basic information

Entry
Database: PDB / ID: 23al
TitleCrystal Structure of Extradiol Dioxygenase (Edo4) in complex with 2-hydroxybiphenyl
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / Extradiol Dioxygenase / Ring cleaving dioxygenase / 2-hydroxybiphenyl
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
2-HYDROXYBIPHENYL / : / DI(HYDROXYETHYL)ETHER / Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesRhizorhabdus wittichii RW1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKayastha, A. / Jangid, K. / 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
DepositionJan 30, 2026Deposition 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
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,19711
Polymers66,3032
Non-polymers8959
Water55831
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)268,78944
Polymers265,2118
Non-polymers3,57836
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area16450 Å2
ΔGint-40 kcal/mol
Surface area83780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.770, 98.770, 152.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 33151.352 Da / Num. of mol.: 2
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) / References: UniProt: A0A9J9LFP0

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Non-polymers , 5 types, 40 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CH9 / 2-HYDROXYBIPHENYL / 1,1'-BIPHENYL-2-OL / 2-PHENYLPHENOL


Mass: 170.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.8 Å3/Da / Density % sol: 56.37 % / Description: Plate shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% w/v PEG4000, 20% v/v glycerol, 0.03 M halogens, and 0.1 M bicine/Trizma base (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 25, 2025
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→29.24 Å / Num. obs: 18973 / % possible obs: 98.04 % / Redundancy: 8.3 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.1879 / Rpim(I) all: 0.06878 / Rrim(I) all: 0.2006 / Net I/σ(I): 14.71
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.6019 / Num. unique obs: 1836 / CC1/2: 0.919 / CC star: 0.979 / Rpim(I) all: 0.2127 / Rrim(I) all: 0.6369 / % possible all: 97.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.24 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.863 / SU B: 30.819 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24875 924 4.9 %RANDOM
Rwork0.21296 ---
obs0.2147 18049 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.069 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 57 31 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164369
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.8156411
X-RAY DIFFRACTIONr_angle_other_deg0.6141.76610024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3375579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.65548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82110734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
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_it0.791.0842328
X-RAY DIFFRACTIONr_mcbond_other0.791.0842328
X-RAY DIFFRACTIONr_mcangle_it1.4221.9392903
X-RAY DIFFRACTIONr_mcangle_other1.4221.9392904
X-RAY DIFFRACTIONr_scbond_it0.7941.1992421
X-RAY DIFFRACTIONr_scbond_other0.7941.1992422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3122.1453509
X-RAY DIFFRACTIONr_long_range_B_refined3.0059.984927
X-RAY DIFFRACTIONr_long_range_B_other2.9999.984926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 65 -
Rwork0.303 1270 -
obs--97.3 %
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)
11.3358-0.03710.25611.9065-0.08451.5010.0009-0.0246-0.11220.0380.0330.25750.0683-0.1933-0.03380.0256-0.0070.01590.09350.01480.049819.976-4.26257.974
21.285-0.1483-0.33681.5635-0.16132.32490.04690.20180.1599-0.23080.0250.0848-0.3279-0.055-0.07190.243-0.0075-0.06350.26380.04940.049323.71215.77218.78
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 297
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B2 - 297
4X-RAY DIFFRACTION2B301 - 305

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