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- PDB-6i5q: Papaver somniferum O-methyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 6i5q
TitlePapaver somniferum O-methyltransferase 1
ComponentsO-methyltransferase 1
KeywordsTRANSFERASE / SAM-dependent O-methyltransferase / Papaver somniferum / scoulerine / tetrahydrocolumbine / noscapine / benzylisoquinoline alkaloid
Function / homology
Function and homology information


tetrahydrocolumbamine 2-O-methyltransferase / benzyl isoquinoline alkaloid biosynthetic process / tetrahydrocolumbamine 2-O-methyltransferase activity / (S)-scoulerine 9-O-methyltransferase / (S)-scoulerine 9-O-methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Scoulerine-9-O-methyltransferase 1 / Scoulerine-9-O-methyltransferase 1
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsCabry, M.P. / Offen, W.A. / Winzer, T. / Li, Y. / Graham, I.A. / Davies, G.J. / Saleh, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2019
Title: Structure of Papaver somniferum O-Methyltransferase 1 Reveals Initiation of Noscapine Biosynthesis with Implications for Plant Natural Product Methylation
Authors: Cabry, M.P. / Offen, W.A. / Winzer, T.H. / Li, Y. / Graham, I.A. / Davies, G.J. / Saleh, P.
History
DepositionNov 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2May 8, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn / struct_conn_type / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase 1
B: O-methyltransferase 1
C: O-methyltransferase 1
D: O-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)171,5534
Polymers171,5534
Non-polymers00
Water00
1
A: O-methyltransferase 1
B: O-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)85,7762
Polymers85,7762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-77 kcal/mol
Surface area26940 Å2
MethodPISA
2
C: O-methyltransferase 1
D: O-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)85,7762
Polymers85,7762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-78 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.004, 112.004, 304.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
O-methyltransferase 1


Mass: 42888.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: O-methyltransferase sequence after cleavage with 3C-protease
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: MT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3PLQ5, UniProt: I3V6A7*PLUS

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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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, sodium citrate, bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→97 Å / Num. obs: 43285 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.052 / Net I/σ(I): 10.7
Reflection shellResolution: 3.05→3.17 Å / Redundancy: 10 % / Rmerge(I) obs: 1.607 / Num. unique obs: 4464 / CC1/2: 0.592 / Rpim(I) all: 0.561 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KYZ

1kyz


Resolution: 3.05→97 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU B: 16.598 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 2.204 / ESU R Free: 0.392
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS SOME UNMODELLED DENSITY BETWEEN THE SIDE CHAINS OF PHE156 AND HIS296 FOR EACH MOLECULE
RfactorNum. reflection% reflectionSelection details
Rfree0.25569 2067 4.8 %RANDOM
Rwork0.21031 ---
obs0.21247 41153 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0.72 Å2-0 Å2
2---1.44 Å20 Å2
3---4.67 Å2
Refinement stepCycle: 1 / Resolution: 3.05→97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 0 0 10068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179266
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.62513977
X-RAY DIFFRACTIONr_angle_other_deg1.2891.56821436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82251364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75723.873426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.399151552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9041531
X-RAY DIFFRACTIONr_chiral_restr0.0690.21367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022044
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_it5.7266.695480
X-RAY DIFFRACTIONr_mcbond_other5.7266.695479
X-RAY DIFFRACTIONr_mcangle_it8.73110.0186836
X-RAY DIFFRACTIONr_mcangle_other8.7310.0176837
X-RAY DIFFRACTIONr_scbond_it5.1726.3584794
X-RAY DIFFRACTIONr_scbond_other5.1726.3574794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.5129.5827139
X-RAY DIFFRACTIONr_long_range_B_refined11.85577.6911218
X-RAY DIFFRACTIONr_long_range_B_other11.85577.69111219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 166 -
Rwork0.366 3004 -
obs--100 %

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