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- PDB-8uzd: The structure of IpCS3, a theobromine methyltransferase from Yerb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uzd | |||||||||
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Title | The structure of IpCS3, a theobromine methyltransferase from Yerba Mate | |||||||||
![]() | IpCS3 | |||||||||
![]() | PLANT PROTEIN / yerba mate / methyltransferase | |||||||||
Function / homology | CAFFEINE / S-ADENOSYL-L-HOMOCYSTEINE![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hernandez Garcia, A. / Nair, S.K. | |||||||||
Funding support | ![]()
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![]() | ![]() 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.R.M. / Nunes, G.L. / Acevedo, R.M. / Burguener, G.F. / Rossi, M. / Zapata, P.D. / Marti, D. ...Authors: Vignale, F.A. / Hernandez Garcia, A. / Modenutti, C.P. / Sosa, E.J. / Defelipe, L.A. / Oliveira, R.R.M. / Nunes, G.L. / Acevedo, R.M. / Burguener, G.F. / Rossi, M. / Zapata, P.D. / Marti, D.A. / Oliveira, G. / Smith, M.N. / Dubs, N.M. / Nair, S.K. / Barkman, T.J. / Turjanski, A.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 112.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
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Components
#1: Protein | Mass: 40816.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.72→2.82 Å / Num. unique obs: 2122 / CC1/2: 0.878 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.721→37.001 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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