+Open data
-Basic information
Entry | Database: PDB / ID: 8ino | ||||||
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Title | Crystal structure of UGT74AN3 in complex UDP and PER | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / Complex | ||||||
Function / homology | Function and homology information quercetin 7-O-glucosyltransferase activity / quercetin 3-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | ||||||
Biological species | Catharanthus roseus (Madagascar periwinkle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Long, F. / Huang, W. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2024 Title: Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3 Authors: Huang, W. / Zhang, X. / Li, J. / Lv, J. / Wang, Y. / He, Y. / Song, J. / Agren, H. / Jiang, R. / Deng, Z. / Long, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ino.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ino.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 8ino.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ino_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ino_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ino_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 8ino_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/8ino ftp://data.pdbj.org/pub/pdb/validation_reports/in/8ino | HTTPS FTP |
-Related structure data
Related structure data | 8inaC 8indC 8invC 8wrjC 8wrkC 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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Unit cell |
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-Components
#1: Protein | Mass: 52543.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Production host: Escherichia coli (E. coli) References: UniProt: A0A385Z961, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-Q30 / |
#3: Chemical | ChemComp-UDP / |
#4: Chemical | ChemComp-TRS / |
#5: 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: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG2000MME, 0.1M Hepes (7.5), 0.2M potassium nitro |
-Data collection
Diffraction | Mean temperature: 203 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.83 Å / Num. obs: 22111 / % possible obs: 99.8 % / Redundancy: 25.7 % / Biso Wilson estimate: 30.58 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 2152 / CC1/2: 0.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.83 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.56 / 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: 2.3→19.83 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.3656 Å / Origin y: 20.5534 Å / Origin z: 75.4261 Å
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Refinement TLS group | Selection details: all |