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- PDB-8uzd: The structure of IpCS3, a theobromine methyltransferase from Yerb... -

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Basic information

Entry
Database: PDB / ID: 8uzd
TitleThe structure of IpCS3, a theobromine methyltransferase from Yerba Mate
ComponentsIpCS3
KeywordsPLANT PROTEIN / yerba mate / methyltransferase
Function / homologyCAFFEINE / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesIlex paraguariensis (yerba mate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.721 Å
AuthorsHernandez Garcia, A. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Elife / Year: 2025
Title: Yerba mate ( Ilex paraguariensis ) genome provides new insights into convergent evolution of caffeine biosynthesis.
Authors: Vignale, F.A. / Hernandez Garcia, A. / Modenutti, C.P. / Sosa, E.J. / Defelipe, L.A. / Oliveira, R. / Nunes, G.L. / Acevedo, R.M. / Burguener, G.F. / Rossi, S.M. / Zapata, P.D. / Marti, D.A. ...Authors: Vignale, F.A. / Hernandez Garcia, A. / Modenutti, C.P. / Sosa, E.J. / Defelipe, L.A. / Oliveira, R. / Nunes, G.L. / Acevedo, R.M. / Burguener, G.F. / Rossi, S.M. / Zapata, P.D. / Marti, D.A. / Sansberro, P. / Oliveira, G. / Catania, E.M. / Smith, M.N. / Dubs, N.M. / Nair, S. / Barkman, T.J. / Turjanski, A.G.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
SupersessionJan 24, 2024ID: 8T2G
Revision 1.1Jan 24, 2024Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Jan 22, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IpCS3
B: IpCS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7906
Polymers81,6332
Non-polymers1,1574
Water86548
1
A: IpCS3
hetero molecules

B: IpCS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7906
Polymers81,6332
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_565y,x+1,-z1
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.675, 82.675, 226.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 26 - 366 / Label seq-ID: 26 - 366

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein IpCS3


Mass: 40816.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ilex paraguariensis (yerba mate) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M NH4SO4, 0.1 M Bis Tris methane pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.72→37.001 Å / Num. obs: 21910 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 25.79
Reflection shellResolution: 2.72→2.82 Å / Num. unique obs: 2122 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.721→37.001 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.584 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2485 1083 4.943 %
Rwork0.1937 20826 -
all0.197 --
obs-21909 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 63.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.035 Å20 Å20 Å2
2---0.035 Å20 Å2
3---0.071 Å2
Refinement stepCycle: LAST / Resolution: 2.721→37.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 0 48 5340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125407
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.6337332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54223.385257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62515939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9681524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024056
X-RAY DIFFRACTIONr_nbd_refined0.2060.22303
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2133
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.25
X-RAY DIFFRACTIONr_mcbond_it4.0276.22653
X-RAY DIFFRACTIONr_mcangle_it6.4159.293304
X-RAY DIFFRACTIONr_scbond_it4.4876.4282754
X-RAY DIFFRACTIONr_scangle_it6.8899.4764028
X-RAY DIFFRACTIONr_lrange_it10.24783.3697870
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.0510370
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083620.0501
12BX-RAY DIFFRACTIONLocal ncs0.083620.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.721-2.7910.369780.2841494X-RAY DIFFRACTION100
2.791-2.8680.387590.2811486X-RAY DIFFRACTION100
2.868-2.9510.36690.2581445X-RAY DIFFRACTION100
2.951-3.0410.351720.2371376X-RAY DIFFRACTION100
3.041-3.1410.28670.2361355X-RAY DIFFRACTION100
3.141-3.2510.306640.2341309X-RAY DIFFRACTION100
3.251-3.3730.258670.2171247X-RAY DIFFRACTION100
3.373-3.5110.281600.2061225X-RAY DIFFRACTION100
3.511-3.6670.261650.2021167X-RAY DIFFRACTION100
3.667-3.8450.219560.2031135X-RAY DIFFRACTION100
3.845-4.0530.252600.1831070X-RAY DIFFRACTION100
4.053-4.2980.226490.1831032X-RAY DIFFRACTION99.9076
4.298-4.5930.197550.159965X-RAY DIFFRACTION99.9021
4.593-4.960.244500.155883X-RAY DIFFRACTION100
4.96-5.4310.233450.166848X-RAY DIFFRACTION100
5.431-6.0690.224410.172762X-RAY DIFFRACTION100
6.069-70.206430.194675X-RAY DIFFRACTION100
7-8.5560.222490.156581X-RAY DIFFRACTION100
8.556-12.0270.135200.136488X-RAY DIFFRACTION100
12.027-37.0010.341140.241283X-RAY DIFFRACTION93.6909

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