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- PDB-7e38: Crystal structure of deoxypodophyllotoxin synthase from Sinopodop... -

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Basic information

Entry
Database: PDB / ID: 7.0E+38
TitleCrystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with yatein and succinate
ComponentsDeoxypodophyllotoxin synthase
KeywordsBIOSYNTHETIC PROTEIN / non-heme iron/2-oxoglutarate enzyme beta-helix fold deoxypodophyllotoxin biosynthesis carbon-carbon bond formation
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 / Chem-YTC / Chem-YTN / Deoxypodophyllotoxin synthase
Similarity search - Component
Biological speciesSinopodophyllum hexandrum (Himalayan mayapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsWu, M.-H. / Chang, W.-c. / Chien, T.-C. / Chan, N.-L.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2811-M-002 -649 - Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2326-B-002 -008 - Taiwan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase.
Authors: Tang, H. / Wu, M.H. / Lin, H.Y. / Han, M.R. / Tu, Y.H. / Yang, Z.J. / Chien, T.C. / Chan, N.L. / Chang, W.C.
History
DepositionFeb 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)74,23010
Polymers72,2802
Non-polymers1,9508
Water8,125451
1
A: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1155
Polymers36,1401
Non-polymers9754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area14080 Å2
MethodPISA
2
B: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1155
Polymers36,1401
Non-polymers9754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-11 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.763, 100.763, 172.602
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-628-

HOH

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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 (E. coli) / Strain (production host): BL21 Star(DE3)pLysS
References: UniProt: A0A0N9HQ36, (-)-deoxypodophyllotoxin synthase

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Non-polymers , 5 types, 459 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-YTC / (3~{S},4~{S})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one


Mass: 400.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-YTN / (3~{R},4~{R})-4-(1,3-benzodioxol-5-ylmethyl)-3-[(3,4,5-trimethoxyphenyl)methyl]oxolan-2-one


Mass: 400.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H24O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.54 Å3/Da / Density % sol: 65.2 % / Description: Rod and plate like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. obs: 62652 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.974 / Rsym value: 0.098 / Net I/σ(I): 17.68
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 3622 / CC1/2: 0.897 / Rsym value: 0.477

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Starting model: 7.0E+37 / Resolution: 2.05→19.89 Å / SU ML: 0.1988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1994 3.19 %
Rwork0.1797 60602 -
obs0.1809 62596 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.53 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4940 0 134 451 5525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235237
X-RAY DIFFRACTIONf_angle_d0.55777101
X-RAY DIFFRACTIONf_chiral_restr0.041761
X-RAY DIFFRACTIONf_plane_restr0.0034911
X-RAY DIFFRACTIONf_dihedral_angle_d7.8367697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.25961400.2124268X-RAY DIFFRACTION96.54
2.1-2.160.23221450.20184248X-RAY DIFFRACTION97.19
2.16-2.220.23051370.19074267X-RAY DIFFRACTION97.2
2.22-2.290.20511380.19464302X-RAY DIFFRACTION97.37
2.29-2.370.27781400.1964274X-RAY DIFFRACTION97.35
2.37-2.470.22621390.20144341X-RAY DIFFRACTION97.69
2.47-2.580.24831390.19454338X-RAY DIFFRACTION97.84
2.58-2.720.25351390.20214298X-RAY DIFFRACTION97.84
2.72-2.890.24051470.20264340X-RAY DIFFRACTION97.78
2.89-3.110.22881450.19484325X-RAY DIFFRACTION97.66
3.11-3.420.2341480.18474370X-RAY DIFFRACTION97.86
3.42-3.910.19881480.15774380X-RAY DIFFRACTION97.5
3.91-4.910.16581440.13974403X-RAY DIFFRACTION97.22
4.91-19.890.19421450.17134448X-RAY DIFFRACTION94.56

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