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- PDB-29ky: L-DOPA extradiol dioxygenase from Beta vulgaris -

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Basic information

Entry
Database: PDB / ID: 29ky
TitleL-DOPA extradiol dioxygenase from Beta vulgaris
Components4,5-DOPA dioxygenase extradiol 1
KeywordsOXIDOREDUCTASE / DODA / betalamic acid / beta vulgaris / L-DOPA extradiol dioxygenase
Function / homologystizolobate synthase / stizolobate synthase activity / Extradiol aromatic ring-opening dioxygenase, DODA-type / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / ferrous iron binding / zinc ion binding / NICKEL (II) ION / 4,5-DOPA dioxygenase extradiol 1
Function and homology information
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsKluza, A. / Milaczewska-Kregiel, A.M. / Borowski, T.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2022/45/B/ST4/01411 Poland
CitationJournal: To Be Published
Title: Structural and mechanistic insight into oxidative ring opening catalyzed by L-DOPA extradiol dioxygenase from Beta vulgaris
Authors: Kluza, A. / Seweryn-Ozog, K. / Hapke, M. / Andrys-Olek, J. / Kachhap, S. / Milaczewska-Kregiel, A.M. / Tataruch, M. / Jahan, F. / Freindl, K. / Korecki, J. / Sarewicz, M. / Osyczka, A. / Borowski, T.
History
DepositionMar 19, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 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: 4,5-DOPA dioxygenase extradiol 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7836
Polymers31,4761
Non-polymers3075
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint4 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.600, 58.520, 52.710
Angle α, β, γ (deg.)90.000, 109.180, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 4,5-DOPA dioxygenase extradiol 1


Mass: 31475.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beta vulgaris (beet) / Gene: DODA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3PFJ9, stizolobate synthase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM magnesium chloride, 200 mM sodium chloride, 0.1 M HEPES 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.11→44.01 Å / Num. obs: 105322 / % possible obs: 99.9 % / Redundancy: 6.53 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.072 / Net I/σ(I): 11.7
Reflection shellResolution: 1.11→1.18 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 16950 / CC1/2: 0.524 / Rrim(I) all: 1.672 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→20.6 Å / SU ML: 0.1376 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.8553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1603 2100 1.99 %
Rwork0.142 103183 -
obs0.1424 105283 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.01 Å2
Refinement stepCycle: LAST / Resolution: 1.11→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 17 387 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692445
X-RAY DIFFRACTIONf_angle_d0.94933361
X-RAY DIFFRACTIONf_chiral_restr0.0874349
X-RAY DIFFRACTIONf_plane_restr0.0107444
X-RAY DIFFRACTIONf_dihedral_angle_d12.9666892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.140.37621390.34626825X-RAY DIFFRACTION99.66
1.14-1.160.33251390.30466811X-RAY DIFFRACTION99.99
1.16-1.20.29451410.27046910X-RAY DIFFRACTION99.97
1.2-1.230.25841390.2456836X-RAY DIFFRACTION99.93
1.23-1.270.25991390.21326851X-RAY DIFFRACTION99.99
1.27-1.320.19851400.19066853X-RAY DIFFRACTION99.94
1.32-1.370.22231390.16776858X-RAY DIFFRACTION99.93
1.37-1.430.18631400.15246868X-RAY DIFFRACTION99.93
1.43-1.510.1391400.12746875X-RAY DIFFRACTION99.97
1.51-1.60.16081400.11326861X-RAY DIFFRACTION99.96
1.6-1.720.131400.10566905X-RAY DIFFRACTION100
1.72-1.90.1551400.10876876X-RAY DIFFRACTION100
1.9-2.170.13261410.11126916X-RAY DIFFRACTION99.97
2.17-2.740.15031400.1316918X-RAY DIFFRACTION99.86
2.74-20.60.13611430.1357020X-RAY DIFFRACTION99.92

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