[English] 日本語
Yorodumi- PDB-8uzd: The structure of IpCS3, a theobromine methyltransferase from Yerb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uzd | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of IpCS3, a theobromine methyltransferase from Yerba Mate | |||||||||
Components | IpCS3 | |||||||||
Keywords | PLANT PROTEIN / yerba mate / methyltransferase | |||||||||
Function / homology | CAFFEINE / S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | |||||||||
Biological species | Ilex paraguariensis (Brazilian-tea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.721 Å | |||||||||
Authors | Hernandez Garcia, A. / Nair, S.K. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: To Be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8uzd.cif.gz | 149.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8uzd.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 8uzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uzd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8uzd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8uzd_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 8uzd_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/8uzd ftp://data.pdbj.org/pub/pdb/validation_reports/uz/8uzd | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
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) |
-Components
#1: Protein | Mass: 40816.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ilex paraguariensis (Brazilian-tea) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.721→37.001 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|