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- PDB-29la: L-DOPA extradiol dioxygenase from Beta vulgaris in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 29la
TitleL-DOPA extradiol dioxygenase from Beta vulgaris in complex with 4-nitrocatechol
Components4,5-DOPA dioxygenase extradiol 1
KeywordsOXIDOREDUCTASE / DODA / betalamic acid / beta vulgaris / L-DOPA extradiol dioxygenase / 4-nitrocatechol
Function / homology
Function and homology information


stizolobate synthase / stizolobate synthase activity / ferrous iron binding / zinc ion binding
Similarity search - Function
Extradiol aromatic ring-opening dioxygenase, DODA-type / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase
Similarity search - Domain/homology
4-NITROCATECHOL / : / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / 4,5-DOPA dioxygenase extradiol 1
Similarity search - Component
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsHapke, M. / Milaczewska-Kregiel, A.M. / Kluza, A. / 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: Hapke, M. / Milaczewska, A.M. / Kluza, 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)32,75220
Polymers31,4761
Non-polymers1,27619
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-6 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.810, 88.810, 94.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-311-

MG

21A-312-

K

31A-442-

HOH

41A-787-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 8 types, 422 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-4NC / 4-NITROCATECHOL


Mass: 155.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium chloride, 0.1 M potassium chloride, 0.1 M PIPES 7.0, 20% PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.13→47.22 Å / Num. obs: 140641 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 20.7 Å2 / CC1/2: 1 / Rrim(I) all: 0.065 / Net I/σ(I): 23.7
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 22468 / CC1/2: 0.421 / Rrim(I) all: 2.737 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→41.69 Å / SU ML: 0.1325 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.3701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1427 2100 1.49 %
Rwork0.1256 138534 -
obs0.1258 140634 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.96 Å2
Refinement stepCycle: LAST / Resolution: 1.13→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 77 403 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732504
X-RAY DIFFRACTIONf_angle_d1.00283427
X-RAY DIFFRACTIONf_chiral_restr0.0877348
X-RAY DIFFRACTIONf_plane_restr0.0091452
X-RAY DIFFRACTIONf_dihedral_angle_d13.9192923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.33871380.3379114X-RAY DIFFRACTION99.75
1.16-1.190.26611380.26989107X-RAY DIFFRACTION99.97
1.19-1.220.25581380.23769127X-RAY DIFFRACTION100
1.22-1.250.24231390.23269129X-RAY DIFFRACTION100
1.25-1.290.20211380.20189159X-RAY DIFFRACTION100
1.29-1.340.18631390.15519156X-RAY DIFFRACTION100
1.34-1.390.16051390.12099166X-RAY DIFFRACTION100
1.39-1.460.11691400.10339215X-RAY DIFFRACTION100
1.46-1.530.12211390.10179166X-RAY DIFFRACTION100
1.53-1.630.12051390.09739210X-RAY DIFFRACTION100
1.63-1.760.11471400.09739251X-RAY DIFFRACTION100
1.76-1.930.12511410.09789274X-RAY DIFFRACTION100
1.93-2.210.1221410.10799310X-RAY DIFFRACTION99.99
2.21-2.790.12981430.11889401X-RAY DIFFRACTION99.99
2.79-41.690.14851480.1319749X-RAY DIFFRACTION99.86

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