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- PDB-9dg7: Tetrahydroprotoberberine N-methyltransferase E204A mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 9dg7
TitleTetrahydroprotoberberine N-methyltransferase E204A mutant in complex with R-reticuline and SAM
ComponentsTetrahydroprotoberberine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase / benzylisoquinoline alkaloid
Function / homology(S)-tetrahydroprotoberberine N-methyltransferase / (S)-tetrahydroprotoberberine N-methyltransferase activity / Mycolic acid cyclopropane synthetase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / S-ADENOSYLMETHIONINE / Tetrahydroprotoberberine N-methyltransferase
Function and homology information
Biological speciesGlaucium flavum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLang, D.E. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: The stereospecific activities of the tetrahydroprotoberberine N-methyltransferase with alternative substrates provide insight into the catalytic mechanisms of benzylisoquinoline alkaloid N-methylation.
Authors: Lang, D.E. / Ng, K.K.S. / Rehman, F. / Morris, J.S. / Facchini, P.J.
History
DepositionSep 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrahydroprotoberberine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4723
Polymers43,7441
Non-polymers7282
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.653, 103.653, 81.817
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 Tetrahydroprotoberberine N-methyltransferase


Mass: 43743.895 Da / Num. of mol.: 1 / Mutation: E204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaucium flavum (plant) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5S8WF76, (S)-tetrahydroprotoberberine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1A4H / (R)-reticuline / (1R)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol


Mass: 329.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Tris-Cl, 15 mM ammonium sulfate, 29% pentaerythritol ethoxylate (15/4 EO/OH), 5% glycerol, 0.5 mM SAM, 0.5 mM R-reticuline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→39.35 Å / Num. obs: 17720 / % possible obs: 98.84 % / Redundancy: 5.6 % / CC1/2: 0.976 / Rsym value: 0.04 / Net I/σ(I): 9.65
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.91 / Num. unique obs: 2461 / CC1/2: 0.724 / Rsym value: 0.333 / % possible all: 97.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.78 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21898 922 5.2 %RANDOM
Rwork0.1578 ---
obs0.16094 16798 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 81.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.5→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 51 246 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122839
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.8383828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.80858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10410528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022132
X-RAY DIFFRACTIONr_gen_planes_other
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_it11.93410.1911360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.7417.061700
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it17.88411.2911479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined22.14291.734519
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 62 -
Rwork0.231 1189 -
obs--96.3 %

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