+Open data
-Basic information
Entry | Database: PDB / ID: 8gxn | ||||||
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Title | The crystal structure of CsFAOMT2 in complex with SAH | ||||||
Components | caffeyl-CoA-O-methyltransferase | ||||||
Keywords | TRANSFERASE / CsFAOMT2 / SAH / O-methyltransferases | ||||||
Function / homology | S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | ||||||
Biological species | Theaceae (tea family) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Zhang, Z.M. / Zhou, Y.E. / Huang, H.S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Characterization of two O-methyltransferases involved in the biosynthesis of O-methylated catechins in tea plant. Authors: Jin, J.Q. / Qu, F.R. / Huang, H. / Liu, Q.S. / Wei, M.Y. / Zhou, Y. / Huang, K.L. / Cui, Z. / Chen, J.D. / Dai, W.D. / Zhu, L. / Yao, M.Z. / Zhang, Z.M. / Chen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gxn.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gxn.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 8gxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/8gxn ftp://data.pdbj.org/pub/pdb/validation_reports/gx/8gxn | HTTPS FTP |
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-Related structure data
Related structure data | 8gxoC 3c3yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26628.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Theaceae (tea family) / Production host: Escherichia alba (bacteria) |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.5M Ammonium Sulfate, 100 mM Sodium Citrate pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.97869 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→64.74 Å / Num. obs: 61963 / % possible obs: 90.6 % / Redundancy: 15 % / Biso Wilson estimate: 15.89 Å2 / CC1/2: 1 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.28→1.35 Å / Num. unique obs: 7996 / CC1/2: 0.898 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C3Y Resolution: 1.34→30.06 Å / SU ML: 0.1326 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5851 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→30.06 Å
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Refine LS restraints |
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LS refinement shell |
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