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- PDB-6gkv: Crystal structure of Coclaurine N-Methyltransferase (CNMT) bound ... -

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Basic information

Entry
Database: PDB / ID: 6gkv
TitleCrystal structure of Coclaurine N-Methyltransferase (CNMT) bound to N-methylheliamine and SAH
ComponentsCoclaurine N-methyltransferase
KeywordsTRANSFERASE / N-methylheliamine / Coclaurine N-Methyltransferase
Function / homology(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase / (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase activity / Mycolic acid cyclopropane synthetase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-F2W / S-ADENOSYL-L-HOMOCYSTEINE / Coclaurine N-methyltransferase
Function and homology information
Biological speciesCoptis japonica (Japanese goldthread)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsDunstan, M.S. / Levy, C.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Structure and Biocatalytic Scope of Coclaurine N-Methyltransferase.
Authors: Bennett, M.R. / Thompson, M.L. / Shepherd, S.A. / Dunstan, M.S. / Herbert, A.J. / Smith, D.R.M. / Cronin, V.A. / Menon, B.R.K. / Levy, C. / Micklefield, J.
History
DepositionMay 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: 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 / _citation_author.name
Revision 1.2May 15, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,3276
Polymers82,1422
Non-polymers1,1854
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-3 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.470, 96.050, 154.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coclaurine N-methyltransferase


Mass: 41070.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coptis japonica (Japanese goldthread) / Gene: cnmt / Production host: Escherichia coli (E. coli)
References: UniProt: Q948P7, (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-F2W / 6,7-dimethoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-2-ium


Mass: 208.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene Glycol 0.1 M HEPES/MOPS (pH 7.4) 37.5 % MPD_PEG 1K/PEG 3350 and 1 mM AdoHcy

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→46.251 Å / Num. obs: 30861 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.35→2.41 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→46.251 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.76
RfactorNum. reflection% reflection
Rfree0.2653 1525 4.94 %
Rwork0.1939 --
obs0.1975 30861 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.47 Å2 / Biso mean: 62.9848 Å2 / Biso min: 22.35 Å2
Refinement stepCycle: final / Resolution: 2.35→46.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5709 0 82 81 5872
Biso mean--63.8 49.3 -
Num. residues----698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095919
X-RAY DIFFRACTIONf_angle_d1.3068006
X-RAY DIFFRACTIONf_chiral_restr0.047874
X-RAY DIFFRACTIONf_plane_restr0.0051011
X-RAY DIFFRACTIONf_dihedral_angle_d16.2342200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.42590.38531400.322326172757100
2.4259-2.51260.35931300.287726112741100
2.5126-2.61320.3331320.272626382770100
2.6132-2.73210.37571330.25826292762100
2.7321-2.87610.32191240.246526422766100
2.8761-3.05630.35381390.232826492788100
3.0563-3.29220.30221430.227726362779100
3.2922-3.62340.2711310.196626712802100
3.6234-4.14740.26671570.171126932850100
4.1474-5.22420.21661420.137527082850100
5.2242-46.260.1941540.16432842299699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.03550.04691.09711.4683-0.13212.08520.0136-0.2503-0.11260.35860.18240.17690.1363-0.4789-0.12960.3247-0.05290.04340.39650.00840.34677.960910.6129-18.4251
21.291-0.53031.48631.4179-1.02431.8184-0.0379-0.21990.21040.14210.0382-0.378-0.09150.3290.07110.2974-0.0409-0.03310.5621-0.03510.534628.535822.3516-19.2582
31.9361-0.3330.80791.56450.15922.1384-0.2806-0.13830.55680.14620.0664-0.4929-0.60430.34960.14960.5114-0.0738-0.1180.38020.00340.607728.359235.9748-22.0354
41.0244-0.40670.36362.1737-0.24582.51050.0499-0.14930.0931-0.0601-0.0038-0.15130.1890.10220.01760.1705-0.00660.00430.2862-0.01890.286219.931518.1456-19.881
50.4765-0.61490.31650.82690.34611.86450.03190.2255-0.0752-0.5322-0.08750.1668-0.0468-0.12810.00060.56870.0766-0.05910.3943-0.01410.39622.071715.662-56.8044
61.9453-0.85390.07841.7396-0.46842.4880.0640.1960.1256-0.4985-0.10660.206-0.5759-0.29620.16080.79790.2544-0.10930.5061-0.08690.4242-8.620237.5817-58.0616
71.441-0.46540.32011.3330.18122.12530.14980.2207-0.0889-0.5338-0.15360.1272-0.0524-0.01690.02790.56450.0866-0.06020.3203-0.02340.29241.91519.861-55.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 66 )A7 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 125 )A67 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 222 )A126 - 222
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 357 )A223 - 357
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 124 )B11 - 124
6X-RAY DIFFRACTION6chain 'B' and (resid 125 through 198 )B125 - 198
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 357 )B199 - 357

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