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- PDB-2efj: The structure of 1,7 dimethylxanthine methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2efj
TitleThe structure of 1,7 dimethylxanthine methyltransferase
Components3,7-dimethylxanthine methyltransferase
KeywordsTRANSFERASE / SAM-dependant methyltransferase / SAH / Theobromine
Function / homology
Function and homology information


caffeine synthase / caffeine synthase activity / alkaloid metabolic process / methylation / metal ion binding
Similarity search - Function
Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THEOBROMINE / S-ADENOSYL-L-HOMOCYSTEINE / 3,7-dimethylxanthine N-methyltransferase
Similarity search - Component
Biological speciesCoffea canephora (robusta coffee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMcCarthy, A.A. / McCarthy, J.G.
Citation
Journal: Plant Physiol. / Year: 2007
Title: The structure of two N-methyltransferases from the caffeine biosynthetic pathway
Authors: McCarthy, A.A. / McCarthy, J.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)
Authors: McCarthy, A.A. / Biget, L. / Lin, C. / Petiard, V. / Tanksley, S.D. / McCarthy, J.G.
History
DepositionFeb 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,7-dimethylxanthine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9713
Polymers43,4061
Non-polymers5652
Water2,630146
1
A: 3,7-dimethylxanthine methyltransferase
hetero molecules

A: 3,7-dimethylxanthine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9426
Polymers86,8122
Non-polymers1,1294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)50.160, 105.630, 140.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the symmetery operations: -x, y, -z+1/2.

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Components

#1: Protein 3,7-dimethylxanthine methyltransferase


Mass: 43406.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coffea canephora (robusta coffee) / Gene: DXMT1 / Plasmid: pProEXHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RIL)
References: UniProt: A4GE70, Transferases; Transferring one-carbon groups; Methyltransferases
#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
#3: Chemical ChemComp-37T / THEOBROMINE / 3,7-DIMETHYLXANTHINE / 3,7-DIMETHYLPURINE-2,6-DIONE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23-28% PEG 3350, 200mM Li2SO4, 100mM Tris-HCl, 2mM DTT, 1mM SAH, 1mM Theobromine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2005
RadiationMonochromator: A double crystal (Si 111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 25506 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.2 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.341 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1297 5.1 %RANDOM
Rwork0.22 ---
all0.223 25059 --
obs-24209 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.306 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--1.42 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 39 146 2904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222853
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9853873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53224.331127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28115467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1781513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022160
X-RAY DIFFRACTIONr_nbd_refined0.2060.21311
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21932
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2790.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.29
X-RAY DIFFRACTIONr_mcbond_it0.7191.51802
X-RAY DIFFRACTIONr_mcangle_it1.17122826
X-RAY DIFFRACTIONr_scbond_it1.74531226
X-RAY DIFFRACTIONr_scangle_it2.5464.51044
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 76 -
Rwork0.301 1707 -
obs--97.06 %
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)
110.1675-1.23024.02674.47540.77371.96220.34950.9509-1.1168-0.10630.43890.39080.2223-0.0407-0.78830.060.0992-0.0018-0.0930.0093-0.03723.93419.53350.24
21.1261-0.74760.71321.0666-0.69322.5178-0.1552-0.28720.07320.3580.27540.0882-0.2113-0.1757-0.1202-0.10630.08760.0724-0.23030.0118-0.17834.43133.86751.92
35.279-0.7196-0.79593.48910.18292.4406-0.3154-0.4022-0.76860.47510.27530.15260.28890.04470.0401-0.00310.15390.0625-0.16680.0721-0.210511.51310.76261.742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 273 - 27
2X-RAY DIFFRACTION2AA28 - 23128 - 231
3X-RAY DIFFRACTION2AA266 - 302266 - 302
4X-RAY DIFFRACTION2AA365 - 379365 - 379
5X-RAY DIFFRACTION3AA232 - 265232 - 265
6X-RAY DIFFRACTION3AA312 - 364312 - 364

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