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- PDB-7e37: Crystal structure of deoxypodophyllotoxin synthase from Sinopodop... -

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Basic information

Entry
Database: PDB / ID: 7.0E+37
TitleCrystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate
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
2-OXOGLUTARIC ACID / : / Deoxypodophyllotoxin synthase
Similarity search - Component
Biological speciesSinopodophyllum hexandrum (Himalayan mayapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWu, M.-H. / Lin, H.-Y. / 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)72,6846
Polymers72,2802
Non-polymers4044
Water8,413467
1
A: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3423
Polymers36,1401
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area14170 Å2
MethodPISA
2
B: Deoxypodophyllotoxin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3423
Polymers36,1401
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.050, 158.287, 51.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-582-

HOH

21B-639-

HOH

31B-720-

HOH

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Components

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.6 % / Description: Rod and plate like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M lithium sulfate, and 25% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 47156 / % possible obs: 93.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.78 Å2 / CC1/2: 0.971 / Rsym value: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.16 / Num. unique obs: 3881 / CC1/2: 0.92 / Rsym value: 0.306 / % possible all: 77.9

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 7.0E+38 / Resolution: 2.09→27.02 Å / SU ML: 0.2283 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1999 4.25 %
Rwork0.1932 45061 -
obs0.1951 47060 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.77 Å2
Refinement stepCycle: LAST / Resolution: 2.09→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 22 467 5391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335053
X-RAY DIFFRACTIONf_angle_d0.59966840
X-RAY DIFFRACTIONf_chiral_restr0.0429741
X-RAY DIFFRACTIONf_plane_restr0.004888
X-RAY DIFFRACTIONf_dihedral_angle_d7.7355658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.27991140.19672571X-RAY DIFFRACTION75.59
2.14-2.20.271240.20612772X-RAY DIFFRACTION81.95
2.2-2.260.26721270.20642895X-RAY DIFFRACTION84.79
2.26-2.330.27041340.20513009X-RAY DIFFRACTION89.26
2.33-2.420.27751370.20423103X-RAY DIFFRACTION91.11
2.42-2.510.26651430.20323214X-RAY DIFFRACTION94.24
2.51-2.630.27571440.20713268X-RAY DIFFRACTION95.6
2.63-2.770.22851480.20683334X-RAY DIFFRACTION97.32
2.77-2.940.28481520.21433397X-RAY DIFFRACTION98.94
2.94-3.170.28021520.20433434X-RAY DIFFRACTION99.69
3.17-3.490.21391530.19713459X-RAY DIFFRACTION99.83
3.49-3.990.20861540.17743469X-RAY DIFFRACTION99.53
3.99-5.020.19131550.15733489X-RAY DIFFRACTION99.35
5.02-27.020.20591620.19033647X-RAY DIFFRACTION98.81

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