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- PDB-9zo1: Crystal structure of deoxypodophyllotoxin synthase (DPS) complexe... -

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Basic information

Entry
Database: PDB / ID: 9zo1
TitleCrystal structure of deoxypodophyllotoxin synthase (DPS) complexed with vanadyl(IV)-oxo, succinate and (-)-hydroxy-yatein
ComponentsDeoxypodophyllotoxin synthase
KeywordsOXIDOREDUCTASE / Oxygenase / Fe/2OG
Function / homology
Function and homology information


(-)-deoxypodophyllotoxin synthase / phenylpropanoid biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / response to wounding / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
: / SUCCINIC ACID / oxovanadium(2+) / Deoxypodophyllotoxin synthase
Similarity search - Component
Biological speciesSinopodophyllum hexandrum (Himalayan mayapple)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMichael, C. / Zheng, Y.-C. / Chang, W.-c.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Biocatalytic Applications and Mechanistic Insights of Deoxypodophyllotoxin Synthase.
Authors: Michael, C. / Zheng, Y.C. / Ruszczycky, M.W. / Chen, N.Q. / Lin, C.H. / Lin, W.Y. / Chang, W.C.
History
DepositionDec 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxypodophyllotoxin synthase
B: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,89214
Polymers72,2802
Non-polymers1,61212
Water11,494638
1
B: Deoxypodophyllotoxin synthase
hetero molecules

A: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,89214
Polymers72,2802
Non-polymers1,61212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area5610 Å2
ΔGint-31 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.927, 87.635, 100.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Deoxypodophyllotoxin synthase / 2-oxoglutarate dependent dioxygenase


Mass: 36140.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinopodophyllum hexandrum (Himalayan mayapple)
Gene: 2-ODD, Phex30848 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0N9HQ36, (-)-deoxypodophyllotoxin synthase

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Non-polymers , 7 types, 650 molecules

#2: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1C3S / (3S,4S)-4-[(S)-(2H-1,3-benzodioxol-5-yl)(hydroxy)methyl]-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one


Mass: 416.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium chloride, 20% (w/v) PEG 3350)

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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: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→17.99 Å / Num. obs: 47608 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 25.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.263 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3450 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→17.99 Å / SU ML: 0.203 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2117 2456 5.17 %
Rwork0.1614 45074 -
obs0.1641 47530 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 2→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 104 638 5764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01695301
X-RAY DIFFRACTIONf_angle_d1.34817176
X-RAY DIFFRACTIONf_chiral_restr0.0776768
X-RAY DIFFRACTIONf_plane_restr0.0115930
X-RAY DIFFRACTIONf_dihedral_angle_d15.8191984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.28621350.23842446X-RAY DIFFRACTION99.23
2.04-2.080.36031360.22562470X-RAY DIFFRACTION99.92
2.08-2.130.2341380.21062483X-RAY DIFFRACTION100
2.13-2.170.25291400.19052456X-RAY DIFFRACTION99.92
2.17-2.230.25741360.18442478X-RAY DIFFRACTION99.96
2.23-2.290.23781460.18042451X-RAY DIFFRACTION99.92
2.29-2.360.26021460.18272476X-RAY DIFFRACTION100
2.36-2.430.22651290.16822497X-RAY DIFFRACTION100
2.43-2.520.25821490.17962483X-RAY DIFFRACTION100
2.52-2.620.2421410.17612481X-RAY DIFFRACTION99.96
2.62-2.740.23271270.17372501X-RAY DIFFRACTION100
2.74-2.880.231320.16142494X-RAY DIFFRACTION100
2.88-3.060.21441210.16352516X-RAY DIFFRACTION100
3.06-3.30.19581240.15452538X-RAY DIFFRACTION100
3.3-3.630.19191330.14512526X-RAY DIFFRACTION100
3.63-4.140.18281190.13422575X-RAY DIFFRACTION99.93
4.15-5.20.15141480.12682549X-RAY DIFFRACTION99.85
5.2-17.990.18931560.16352654X-RAY DIFFRACTION99.54

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