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- PDB-6p3m: Tetrahydroprotoberberine N-methyltransferase in complex with S-ad... -

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Basic information

Entry
Database: PDB / ID: 6p3m
TitleTetrahydroprotoberberine N-methyltransferase in complex with S-adenosylhomocysteine
Componentstetrahydroprotoberberine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesGlaucium flavum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLang, D.E. / Morris, J.S. / Rowley, M. / Torres, M.A. / Maksimovich, V.A. / Facchini, P.J. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure-function studies of tetrahydroprotoberberineN-methyltransferase reveal the molecular basis of stereoselective substrate recognition.
Authors: Lang, D.E. / Morris, J.S. / Rowley, M. / Torres, M.A. / Maksimovich, V.A. / Facchini, P.J. / Ng, K.K.S.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: tetrahydroprotoberberine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2823
Polymers43,8021
Non-polymers4802
Water5,639313
1
A: tetrahydroprotoberberine N-methyltransferase
hetero molecules

A: tetrahydroprotoberberine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5656
Polymers87,6042
Non-polymers9614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area2630 Å2
ΔGint-53 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.693, 103.693, 82.812
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: 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: (S)-tetrahydroprotoberberine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium Sulfate, Glycerol, Pentaerythritol ethoxylate (15/4 EO/OH), Tris-Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→37.6 Å / Num. obs: 48045 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 1 / Rrim(I) all: 0.056 / Rsym value: 0.055 / Net I/σ(I): 26.93
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.18 / Num. unique obs: 3522 / CC1/2: 0.773 / Rrim(I) all: 1.17 / Rsym value: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOK

5kok


Resolution: 1.8→37.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.89 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.19694 2485 5.2 %RANDOM
Rwork0.1623 ---
obs0.16405 45474 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 36.506 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.8→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 31 313 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122856
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6273854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32324.514144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.945158
X-RAY DIFFRACTIONr_chiral_restr0.0880.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022149
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_it4.9294.2941380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.8485.9691732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0614.951474
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.45644.984429
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 176 -
Rwork0.247 3335 -
obs--99.97 %

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