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- PDB-29kz: L-DOPA extradiol dioxygenase from Beta vulgaris in complex with L-DOPA -

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Basic information

Entry
Database: PDB / ID: 29kz
TitleL-DOPA extradiol dioxygenase from Beta vulgaris in complex with L-DOPA
Components4,5-DOPA dioxygenase extradiol 1
KeywordsOXIDOREDUCTASE / DODA / betalamic acid / beta vulgaris / L-DOPA extradiol dioxygenase
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
3,4-DIHYDROXYPHENYLALANINE / NICKEL (II) ION / 4,5-DOPA dioxygenase extradiol 1
Similarity search - Component
Biological speciesBeta vulgaris (beet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKluza, A. / Hapke, M. / Seweryn-Ozog, K. / 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. / Hapke, M. / Seweryn-Ozog, K. / Milaczewska, A.M. / 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)32,37714
Polymers31,4761
Non-polymers90113
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint7 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.710, 88.710, 94.000
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-305-

MG

21A-459-

HOH

31A-516-

HOH

41A-663-

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 , 5 types, 276 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DAH / 3,4-DIHYDROXYPHENYLALANINE / L-DOPA


Type: L-peptide linking / Mass: 197.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM magnesium chloride, 0.2 M ammonium sulphate, 0.1 M MES pH 6.5, 25 % PEG 3350

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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: Apr 30, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 35359 / % possible obs: 99.9 % / Redundancy: 17.7 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.176 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5605 / CC1/2: 0.5 / Rrim(I) all: 2.93 / % possible all: 99.8

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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: 1.8→39.67 Å / SU ML: 0.1922 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 1768 5 %
Rwork0.1625 33587 -
obs0.1642 35355 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 56 263 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672275
X-RAY DIFFRACTIONf_angle_d0.83993101
X-RAY DIFFRACTIONf_chiral_restr0.0542325
X-RAY DIFFRACTIONf_plane_restr0.0075399
X-RAY DIFFRACTIONf_dihedral_angle_d12.4975804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.32981330.28672538X-RAY DIFFRACTION99.63
1.85-1.90.28781330.25652532X-RAY DIFFRACTION100
1.9-1.960.27391340.25142544X-RAY DIFFRACTION99.96
1.96-2.030.23581330.21042528X-RAY DIFFRACTION100
2.03-2.120.24271350.19442555X-RAY DIFFRACTION99.96
2.12-2.210.2261350.16772559X-RAY DIFFRACTION100
2.21-2.330.21191340.16422556X-RAY DIFFRACTION99.93
2.33-2.480.17981350.1552560X-RAY DIFFRACTION99.93
2.48-2.670.21341360.14472581X-RAY DIFFRACTION100
2.67-2.930.16631360.14562595X-RAY DIFFRACTION100
2.93-3.360.1961380.15172610X-RAY DIFFRACTION100
3.36-4.230.15021390.13692645X-RAY DIFFRACTION100
4.23-39.670.1931470.1572784X-RAY DIFFRACTION99.8
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)
12.409894531770.107988561041-0.3206532307782.348461660650.2286571586472.11138412969-0.0419056510208-0.0003050836655450.1577635779990.114460603380.0499239127108-0.195928391333-0.1205787502950.157201914778-0.007729442453310.2178854403510.00489722032336-0.03215384682250.236945713482-0.004380028870330.24113349035427.9765364382-4.43098756627-14.1998853735
21.65803285898-0.428959911301-0.1358360040861.559027320390.3331694429161.02132848451-0.0325098338297-0.2146232541840.06141939914670.207573851160.0715553260227-0.0473133311209-0.02724387377570.00127066780713-0.03968870992360.2823263446160.001115105059950.01004943101020.2787807829820.00190255719620.26318255732920.8025520475-6.41081527612-10.1322048074
32.06742921530.6197660122430.291540442113.07927544475-0.8495093048255.89009957177-0.1281747860250.4103284522340.102315961376-0.4184396381060.1695377906620.01209666837910.113425451279-0.0117591640223-0.03377671746310.244786513052-0.03965496516520.01165246709030.3449844449030.0323025742650.3079203393421.65401819283.25361328409-29.3622944704
42.482598043350.0708351798457-0.4569436417252.204725749150.3584869682293.22631525626-0.04018243084440.2480799353950.354943173076-0.03677828503830.08268912093630.0588783876868-0.178558023043-0.179402775218-0.0230055935420.197521349485-0.006274519260610.0003939052064170.1745081266510.04994804989730.22909693107419.49424871796.67094663195-22.6752456046
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 78)10 - 781 - 69
22chain 'A' and (resid 79 through 170 )79 - 17070 - 161
33chain 'A' and (resid 171 through 210 )171 - 210162 - 201
44chain 'A' and (resid 211 through 275 )211 - 275202 - 266

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