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- PDB-5kok: Pavine N-methyltransferase in complex with Tetrahydropapaverine a... -

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Basic information

Entry
Database: PDB / ID: 5kok
TitlePavine N-methyltransferase in complex with Tetrahydropapaverine and S-adenosylhomocysteine pH 7.25
ComponentsPavine N-methyltransferase
KeywordsTRANSFERASE / benzylisoquinoline alkaloid biosynthesis
Function / homology
Function and homology information


pavine N-methyltransferase / methyltransferase activity / methylation / cytoplasm
Similarity search - Function
Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-R9T / Chem-S9T / S-ADENOSYL-L-HOMOCYSTEINE / Pavine N-methyltransferase
Similarity search - Component
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å
AuthorsTorres, M.A. / Hoffarth, E. / Eugenio, L. / Savtchouk, J. / Chen, X. / Morris, J. / Facchini, P.J. / Ng, K.K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)262089 Canada
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Studies of Pavine N-Methyltransferase from Thalictrum flavum Reveal Novel Insights into Substrate Recognition and Catalytic Mechanism.
Authors: Torres, M.A. / Hoffarth, E. / Eugenio, L. / Savtchouk, J. / Chen, X. / Morris, J.S. / Facchini, P.J. / Ng, K.K.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Pavine N-methyltransferase
B: Pavine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0168
Polymers92,8742
Non-polymers2,1426
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-5 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.776, 71.637, 95.226
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pavine N-methyltransferase / PfPavNMT


Mass: 46436.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalictrum flavum subsp. glaucum (plant)
Plasmid: pRSETC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: C3SBW0, pavine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#3: Chemical ChemComp-S9T / (1~{S})-1-[(3,4-dimethoxyphenyl)methyl]-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline / S-Tetrahydropapaverine


Mass: 343.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25NO4
#4: Chemical ChemComp-R9T / (1~{R})-1-[(3,4-dimethoxyphenyl)methyl]-6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline / R-Tetrahydropapaverine


Mass: 343.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 1.95 Å3/Da / Density % sol: 36.91 % / Description: Plate-like, 0.2x0.2 mm
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 210 g/L polyethylene glycol 3350, 100 mM sodium HEPES pH 7.25, 75 mM potassium chloride, 120 g/L glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.792→39.297 Å / Num. obs: 65359 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.169 / Rsym value: 0.169 / Net I/σ(I): 24.7
Reflection shellResolution: 1.792→1.8179 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 7.57 / CC1/2: 0.982 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSNov 11, 2013data reduction
XSCALENov 11, 2013data scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KN4

5kn4


Resolution: 1.792→39.297 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.17
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3343 5.11 %Random
Rwork0.1633 ---
obs0.1652 65359 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.792→39.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5689 0 152 535 6376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075985
X-RAY DIFFRACTIONf_angle_d0.8858076
X-RAY DIFFRACTIONf_dihedral_angle_d14.7953496
X-RAY DIFFRACTIONf_chiral_restr0.057865
X-RAY DIFFRACTIONf_plane_restr0.005996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7923-1.81790.24031270.20762090X-RAY DIFFRACTION81
1.8179-1.84510.24521540.18522590X-RAY DIFFRACTION98
1.8451-1.87390.22381290.17922614X-RAY DIFFRACTION99
1.8739-1.90460.2021450.17642626X-RAY DIFFRACTION99
1.9046-1.93750.23021500.1772591X-RAY DIFFRACTION99
1.9375-1.97270.24511370.16762580X-RAY DIFFRACTION98
1.9727-2.01060.22131560.16172584X-RAY DIFFRACTION98
2.0106-2.05170.18461320.15752594X-RAY DIFFRACTION97
2.0517-2.09630.18671140.15692547X-RAY DIFFRACTION96
2.0963-2.1450.22851370.15642623X-RAY DIFFRACTION99
2.145-2.19870.18591350.1592591X-RAY DIFFRACTION99
2.1987-2.25810.20261380.16422644X-RAY DIFFRACTION99
2.2581-2.32460.2141520.16882593X-RAY DIFFRACTION99
2.3246-2.39960.21471430.16822590X-RAY DIFFRACTION98
2.3996-2.48530.2211390.17762569X-RAY DIFFRACTION96
2.4853-2.58480.24011290.17472583X-RAY DIFFRACTION97
2.5848-2.70240.24361380.17612627X-RAY DIFFRACTION99
2.7024-2.84490.19741470.17562596X-RAY DIFFRACTION99
2.8449-3.02310.22771400.17072622X-RAY DIFFRACTION99
3.0231-3.25640.20271390.16792569X-RAY DIFFRACTION96
3.2564-3.58390.19861210.15962684X-RAY DIFFRACTION99
3.5839-4.1020.15691450.14322625X-RAY DIFFRACTION99
4.102-5.16620.17391390.13822609X-RAY DIFFRACTION97
5.1662-39.30650.16461570.16962675X-RAY DIFFRACTION98

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