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- PDB-9dg9: Tetrahydroprotoberberine N-methyltransferase E207A mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 9dg9
TitleTetrahydroprotoberberine N-methyltransferase E207A 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: 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

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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)44,6956
Polymers43,7441
Non-polymers9515
Water6,485360
1
A: Tetrahydroprotoberberine N-methyltransferase
hetero molecules

A: Tetrahydroprotoberberine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,39112
Polymers87,4882
Non-polymers1,90310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area3330 Å2
ΔGint-81 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.693, 103.693, 82.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tetrahydroprotoberberine N-methyltransferase


Mass: 43743.895 Da / Num. of mol.: 1 / Mutation: E207A
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

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Non-polymers , 6 types, 365 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% Pentaerythritol ethoxylate (15/4 EO/OH), 15 mM ammonium sulfate, 6% Glycerol, 0.5 mM (R)-reticuline, 0.5 mM SAM, 0.1 mM Tris-Cl

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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→39.46 Å / Num. obs: 67813 / % possible obs: 99.81 % / Redundancy: 13.4 % / CC1/2: 1 / Rsym value: 0.016 / Net I/σ(I): 14.84
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2720 / CC1/2: 0.698 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.459 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.543 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.071 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1958 3468 5.114 %
Rwork0.1777 64345 -
all0.179 --
obs-67813 99.863 %
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: 43.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.019 Å20.009 Å20 Å2
2--0.019 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 63 360 3116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122917
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.8343945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.56458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06210542
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.53710135
X-RAY DIFFRACTIONr_chiral_restr0.0870.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022212
X-RAY DIFFRACTIONr_nbd_refined0.2010.21406
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.235
X-RAY DIFFRACTIONr_mcbond_it3.9135.11401
X-RAY DIFFRACTIONr_mcangle_it4.9988.541767
X-RAY DIFFRACTIONr_scbond_it6.5845.9441516
X-RAY DIFFRACTIONr_scangle_it9.0669.8952178
X-RAY DIFFRACTIONr_lrange_it11.59146.0034748
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
1.6-1.6420.2762580.26347200.26449780.9450.9491000.263
1.642-1.6860.272210.24546010.24648220.9480.9581000.245
1.686-1.7350.2522300.24944850.24947160.9540.95699.97880.249
1.735-1.7890.2432550.20943440.21145990.9640.9711000.209
1.789-1.8470.2152140.1942040.19144180.9720.9771000.19
1.847-1.9120.2382180.23240680.23243000.9650.96299.67440.232
1.912-1.9840.291950.26439260.26541350.9470.94699.66140.264
1.984-2.0640.2251990.19838280.240270.9680.9751000.198
2.064-2.1560.221900.21536200.21538160.9620.96199.84280.215
2.156-2.2610.2441790.22134830.22236860.8990.92299.34890.221
2.261-2.3830.2171640.18733270.18935080.9720.97299.51540.187
2.383-2.5270.2282000.1831070.18333080.970.97599.96980.18
2.527-2.70.1911700.17529630.17631340.9770.9799.96810.175
2.7-2.9160.1741550.16427740.16429300.9810.98399.96590.164
2.916-3.1920.1671350.16425540.16426890.9820.9831000.164
3.192-3.5660.1611300.14923160.1524500.9840.98599.83670.149
3.566-4.1120.1641270.13920450.14121750.9820.98899.86210.139
4.112-5.0230.1641010.13817560.1418570.9820.9881000.138
5.023-7.0460.178770.17513980.17514750.9790.9811000.175
7.046-39.4590.197500.1678240.1698750.9720.98199.88570.167

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