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- PDB-5kn4: Pavine N-methyltransferase apoenzyme pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 5kn4
TitlePavine N-methyltransferase apoenzyme pH 6.0
ComponentsPavine N-methyltransferase
KeywordsTRANSFERASE / benzylisoquinoline alkaloid biosynthesis
Function / homologypavine N-methyltransferase / Mycolic acid cyclopropane synthetase / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / cytoplasm / Pavine N-methyltransferase
Function and homology information
Biological speciesThalictrum flavum subsp. glaucum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 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 27, 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 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)92,8742
Polymers92,8742
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-4 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.743, 72.301, 97.136
Angle α, β, γ (deg.)90.00, 99.75, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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 Å3/Da / Density % sol: 38.58 % / Description: Plate-like, 0.1x0.2 mm
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 230 g/L pentaerythritol ethoxylate (15/4 EO/OH), 50 mM Bis-tris-Cl pH 6.0, 70 mM ammonium sulfate, 120 g/L glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.984, 0.97915, 0.95369, 0.97932
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2014 / Details: collimating mirror / toroidal focusing mirror
RadiationMonochromator: double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
20.979151
30.953691
40.979321
ReflectionResolution: 1.99→40 Å / Num. obs: 47373 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.752 / % possible all: 78.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNov 11, 2013data reduction
XSCALENov 11, 2013data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→38.946 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 2394 5.06 %Random
Rwork0.1956 ---
obs0.1984 47300 93.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→38.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 0 203 5420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115334
X-RAY DIFFRACTIONf_angle_d1.1647181
X-RAY DIFFRACTIONf_dihedral_angle_d16.131969
X-RAY DIFFRACTIONf_chiral_restr0.052780
X-RAY DIFFRACTIONf_plane_restr0.006894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9896-2.03020.31741040.30751937X-RAY DIFFRACTION69
2.0302-2.07430.35161480.28622491X-RAY DIFFRACTION90
2.0743-2.12260.31941440.23972724X-RAY DIFFRACTION96
2.1226-2.17570.27731440.22752698X-RAY DIFFRACTION97
2.1757-2.23450.28711530.2192743X-RAY DIFFRACTION97
2.2345-2.30020.29311360.21122684X-RAY DIFFRACTION97
2.3002-2.37450.26981620.21772722X-RAY DIFFRACTION96
2.3745-2.45930.3191430.21132655X-RAY DIFFRACTION95
2.4593-2.55780.31741270.21632572X-RAY DIFFRACTION91
2.5578-2.67420.24511580.20032753X-RAY DIFFRACTION98
2.6742-2.81510.26191360.20792768X-RAY DIFFRACTION98
2.8151-2.99140.26841400.19872741X-RAY DIFFRACTION97
2.9914-3.22230.26391460.20852606X-RAY DIFFRACTION92
3.2223-3.54640.22271300.19092673X-RAY DIFFRACTION95
3.5464-4.05910.24011260.17692785X-RAY DIFFRACTION97
4.0591-5.11220.21341460.16152593X-RAY DIFFRACTION92
5.1122-38.95370.23331510.18642761X-RAY DIFFRACTION95

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