+Open data
-Basic information
Entry | Database: PDB / ID: 8inh | ||||||
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Title | ZjOGT3, flavonoid 7,4'-di-O-glycosyltransferase | ||||||
Components | Glycosyltransferase | ||||||
Keywords | PLANT PROTEIN / glycosyltransferase | ||||||
Function / homology | URIDINE-5'-DIPHOSPHATE / Uncharacterized protein Function and homology information | ||||||
Biological species | Ziziphus jujuba var. spinosa (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wang, Z.L. / Wang, H.D. / Li, F.D. / Ye, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Functional characterization, structural basis, and regio-selectivity control of a promiscuous flavonoid 7,4'-di- O -glycosyltransferase from Ziziphus jujuba var. spinosa. Authors: Wang, Z.L. / Wei, W. / Wang, H.D. / Zhou, J.J. / Wang, H.T. / Chen, K. / Wang, R.S. / Li, F.D. / Qiao, X. / Zhou, H. / Liang, Y. / Ye, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8inh.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8inh.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 8inh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/8inh ftp://data.pdbj.org/pub/pdb/validation_reports/in/8inh | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
#1: Protein | Mass: 53614.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ziziphus jujuba var. spinosa (plant) / Gene: FEM48_Zijuj09G0128800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A978UT44 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium acetate trihydrate, 26% w/v PEG 4000, 10 mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.73 Å / Num. obs: 35988 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.77 Å2 / CC1/2: 0.984 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 35988 / CC1/2: 0.984 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→51.73 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→51.73 Å
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Refine LS restraints |
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LS refinement shell |
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