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- PDB-5o7y: Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in compl... -

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Basic information

Entry
Database: PDB / ID: 5o7y
TitleThebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with succinate
ComponentsThebaine 6-O-demethylase
KeywordsOXIDOREDUCTASE / 2-oxoglutarate dependent dioxygenase / morphine biosynthesis / oripavine / thebaine
Function / homology
Function and homology information


thebaine 6-O-demethylase / (S)-tetrahydroprotoberberine N-methyltransferase activity / thebaine 6-O-demethylase activity / morphine biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / 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
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Thebaine 6-O-demethylase
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKluza, A. / Niedzialkowska, E. / Kurpiewska, K. / Porebski, P.J. / Borowski, T.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre, PolandUMO-2014/14/E/NZ1/00053 Poland
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway.
Authors: Kluza, A. / Niedzialkowska, E. / Kurpiewska, K. / Wojdyla, Z. / Quesne, M. / Kot, E. / Porebski, P.J. / Borowski, T.
History
DepositionJun 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thebaine 6-O-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,38122
Polymers40,9371
Non-polymers1,44421
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint44 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.231, 87.028, 94.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thebaine 6-O-demethylase


Mass: 40936.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: T6ODM, DIOX1 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Magic / References: UniProt: D4N500, thebaine 6-O-demethylase

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Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 125 mM sodium succinate, 22% PEG 3350. Concentration of protein 37.5 mg/ml.

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.97→41.51 Å / Num. obs: 28189 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 17.71
Reflection shellResolution: 1.97→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.271 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XAE

4xae


Resolution: 1.97→41.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.396 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20674 1364 4.9 %RANDOM
Rwork0.16265 ---
obs0.16485 26620 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.97→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 91 335 3206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192978
X-RAY DIFFRACTIONr_bond_other_d0.0020.022843
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9943997
X-RAY DIFFRACTIONr_angle_other_deg0.91936634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16225.403124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5751511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213217
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8462.8221458
X-RAY DIFFRACTIONr_mcbond_other1.8432.821457
X-RAY DIFFRACTIONr_mcangle_it3.0824.2171826
X-RAY DIFFRACTIONr_mcangle_other3.0834.2181827
X-RAY DIFFRACTIONr_scbond_it1.7852.9781520
X-RAY DIFFRACTIONr_scbond_other1.7842.9781520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9174.3532166
X-RAY DIFFRACTIONr_long_range_B_refined5.57533.0163264
X-RAY DIFFRACTIONr_long_range_B_other5.37332.4523186
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 90 -
Rwork0.214 1846 -
obs--95.18 %

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