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- PDB-9dge: Tetrahydroprotoberberine N-methyltransferase product complex with... -

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Basic information

Entry
Database: PDB / ID: 9dge
TitleTetrahydroprotoberberine N-methyltransferase product complex with dextromethorphan 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: 1.6 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
Revision 1.1Nov 19, 2025Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)44,5684
Polymers43,8021
Non-polymers7663
Water6,179343
1
A: Tetrahydroprotoberberine N-methyltransferase
hetero molecules

A: Tetrahydroprotoberberine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1368
Polymers87,6042
Non-polymers1,5326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2520 Å2
ΔGint-52 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.992, 103.992, 82.536
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

21A-746-

HOH

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Components

#1: Protein Tetrahydroprotoberberine N-methyltransferase


Mass: 43801.926 Da / Num. of mol.: 1
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-4NQ / Dextromethorphan / 3-methoxy-17-methyl-9alpha,13alpha,14alpha-morphinan


Mass: 271.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 10 mM ammonium sulfate, 5% glycerol, 0.5 mM dextromethorphan, 0.5 mM SAM

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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: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→39.53 Å / Num. obs: 68044 / % possible obs: 99.88 % / Redundancy: 13.4 % / CC1/2: 1 / Rsym value: 0.011 / Net I/σ(I): 19.52
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2684 / CC1/2: 0.791 / Rsym value: 0.312 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.53 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.316 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.071 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1912 3480 5.114 %
Rwork0.1707 64563 -
all0.172 --
obs-68043 99.877 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 38.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.088 Å20.044 Å20 Å2
2--0.088 Å2-0 Å2
3----0.285 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 52 343 3116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123049
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.8364143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.81759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3710571
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.70310146
X-RAY DIFFRACTIONr_chiral_restr0.0890.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022348
X-RAY DIFFRACTIONr_nbd_refined0.190.21444
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.235
X-RAY DIFFRACTIONr_mcbond_it3.5784.4951467
X-RAY DIFFRACTIONr_mcangle_it5.0597.4941867
X-RAY DIFFRACTIONr_scbond_it5.7715.2341582
X-RAY DIFFRACTIONr_scangle_it8.3568.7332276
X-RAY DIFFRACTIONr_lrange_it10.29141.2344944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.2792390.24447140.24649610.9450.95999.83870.244
1.642-1.6860.2582470.22646040.22848530.9560.96699.95880.226
1.686-1.7350.2332460.20744660.20847240.9630.97299.7460.207
1.735-1.7880.2022480.19443460.19445940.9740.9771000.194
1.788-1.8470.2172470.18842030.1944540.970.97899.91020.188
1.847-1.9120.2162160.1940950.19243110.9720.9781000.19
1.912-1.9840.1952130.18739620.18841770.9750.97899.95210.187
1.984-2.0640.2082120.18538040.18640160.9740.9791000.185
2.064-2.1560.1982110.18636350.18738470.9730.97899.9740.186
2.156-2.2610.181870.17735190.17737140.9810.98199.78460.177
2.261-2.3830.1991760.17533100.17734860.9760.981000.175
2.383-2.5270.2131890.18431570.18533460.970.9791000.184
2.527-2.70.2031320.17529990.17631310.9750.9811000.175
2.7-2.9160.2081700.17627680.17729460.9740.98199.72840.176
2.916-3.1920.1911270.16625770.16827040.9780.9831000.166
3.192-3.5660.1641140.15223360.15224500.9850.9861000.152
3.566-4.1120.1531040.13920710.13921900.9830.98899.31510.139
4.112-5.0230.156850.13817670.13818550.9860.98899.83830.138
5.023-7.0470.206800.18613980.18714780.9760.9781000.186
7.047-39.530.174370.1798320.1798840.980.97798.30320.179

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