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- PDB-2eg5: The structure of xanthosine methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2eg5
TitleThe structure of xanthosine methyltransferase
ComponentsXanthosine methyltransferase
KeywordsTRANSFERASE / SAM-dependant N-methyltransferase / xanthosine / SAH
Function / homology
Function and homology information


7-methylxanthosine synthase / alkaloid metabolic process / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase, alpha-helical capping domain / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / 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 / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / 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
S-ADENOSYL-L-HOMOCYSTEINE / Chem-XTS / 7-methylxanthosine synthase 1
Similarity search - Component
Biological speciesCoffea canephora (robusta coffee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 28, 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 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Xanthosine methyltransferase
C: Xanthosine methyltransferase
E: Xanthosine methyltransferase
G: Xanthosine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,25112
Polymers167,5774
Non-polymers2,6758
Water8,989499
1
A: Xanthosine methyltransferase
C: Xanthosine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1266
Polymers83,7882
Non-polymers1,3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-14 kcal/mol
Surface area28460 Å2
MethodPISA
2
E: Xanthosine methyltransferase
G: Xanthosine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1266
Polymers83,7882
Non-polymers1,3374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-14 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.590, 119.800, 116.400
Angle α, β, γ (deg.)90.00, 102.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12A
22C
32E
42G

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA14 - 36714 - 367
21GLYGLYPROPROCB14 - 36714 - 367
31GLYGLYPROPROEC14 - 36714 - 367
41GLYGLYPROPROGD14 - 36714 - 367
12SAHSAHXTSXTSAE - F501 - 502
22SAHSAHXTSXTSCG - H1501 - 1502
32SAHSAHXTSXTSEI - J2501 - 2502
42SAHSAHXTSXTSGK - L3501 - 3502

NCS ensembles :
ID
1
2
DetailsChain A and C form a biological dimer / Chain E and G form a biological dimer

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Components

#1: Protein
Xanthosine methyltransferase


Mass: 41894.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coffea canephora (robusta coffee) / Gene: XMT1 / Plasmid: pProEXHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RIL)
References: UniProt: A4GE69, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-XTS / 9-[(2R,3R,4S,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)OXOLAN-2-YL]-3H-PURINE-2,6-DIONE / XANTHOSINE / 9-BETA-D-RIBOFURANOSYLXANTHINE / Xanthosine


Type: RNA linking / Mass: 284.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 200mM Li2SO4, 100mM Tris-HCl, 1mM SAH, 1mM xanthosine, 2mM DTT, 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 12, 2005
RadiationMonochromator: Khozu double crystal (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 75624 / Num. obs: 74901 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3 / Num. unique all: 10071 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EFJ

2efj


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 17.957 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3830 5.1 %RANDOM
Rwork0.23 ---
obs0.233 71794 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.845 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.42 Å2
2---1.88 Å20 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10668 0 184 499 11351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211184
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.99815174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82651387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84524.113462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.096151885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8741552
X-RAY DIFFRACTIONr_chiral_restr0.1140.21737
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028312
X-RAY DIFFRACTIONr_nbd_refined0.2330.25231
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2585
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.212
X-RAY DIFFRACTIONr_mcbond_it0.8971.57083
X-RAY DIFFRACTIONr_mcangle_it1.519211128
X-RAY DIFFRACTIONr_scbond_it2.09334661
X-RAY DIFFRACTIONr_scangle_it3.1624.54033
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2603tight positional0.060.05
12E2603tight positional0.080.05
13A2603tight positional0.070.05
14C2603tight positional0.060.05
22C46tight positional0.040.05
22G46tight positional0.030.05
22A46tight positional0.030.05
22C46tight positional0.040.05
11A2603tight thermal0.170.5
12E2603tight thermal0.160.5
13A2603tight thermal0.130.5
14C2603tight thermal0.170.5
22C46tight thermal0.120.5
22G46tight thermal0.090.5
22A46tight thermal0.110.5
22C46tight thermal0.170.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 286 -
Rwork0.34 5315 -
obs--98.04 %
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)
11.27990.8588-0.45742.4011-0.60950.9554-0.0670.0368-0.0237-0.09160.051-0.2430.0119-0.02960.016-0.13280.01090.0121-0.1077-0.025-0.156832.057991.6382109.4734
20.85520.54610.112.80490.5040.5729-0.05310.05810.2147-0.20870.03790.53350.02180.02730.0152-0.11880.0056-0.0009-0.09090.0743-0.03985.212262.548108.834
31.04430.41160.50013.14620.94771.522-0.0279-0.0915-0.0027-0.11640.01980.28020.0013-0.02860.0082-0.06230.0055-0.006-0.02680.02310.0033-11.323930.376853.0587
42.1185-0.00730.4552.1829-0.6870.9984-0.0540.43960.1364-0.1720.0057-0.37890.00360.10040.0483-0.02810.01870.01920.1114-0.0209-0.165915.524459.077851.3167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 36714 - 367
2X-RAY DIFFRACTION1AE - F501 - 502
3X-RAY DIFFRACTION2CB14 - 36714 - 367
4X-RAY DIFFRACTION2CG - H1501 - 1502
5X-RAY DIFFRACTION3EC14 - 36714 - 367
6X-RAY DIFFRACTION3EI - J2501 - 2502
7X-RAY DIFFRACTION4GD14 - 36714 - 367
8X-RAY DIFFRACTION4GK - L3501 - 3502

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