+Open data
-Basic information
Entry | Database: PDB / ID: 7w0k | ||||||||||||
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Title | plant glycosyltransferase | ||||||||||||
Components | Glycosyltransferase | ||||||||||||
Keywords | TRANSFERASE / UGT74AN2 Complex with UDP | ||||||||||||
Function / homology | Function and homology information quercetin 7-O-glucosyltransferase activity / quercetin 3-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding Similarity search - Function | ||||||||||||
Biological species | Calotropis gigantea (mudar) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||||||||
Authors | Wei, H. / Feng, L. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Functional and Structural Dissection of a Plant Steroid 3-O-Glycosyltransferase Facilitated the Engineering Enhancement of Sugar Donor Promiscuity Authors: Huang, W. / He, Y. / 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 | 7w0k.cif.gz | 191.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w0k.ent.gz | 148 KB | Display | PDB format |
PDBx/mmJSON format | 7w0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w0k_validation.pdf.gz | 792.8 KB | Display | wwPDB validaton report |
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Full document | 7w0k_full_validation.pdf.gz | 796.3 KB | Display | |
Data in XML | 7w0k_validation.xml.gz | 18 KB | Display | |
Data in CIF | 7w0k_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/7w0k ftp://data.pdbj.org/pub/pdb/validation_reports/w0/7w0k | HTTPS FTP |
-Related structure data
Related structure data | 7w09C 7w0zC 7w10C 7w11C 7w1bC 7w1hC 6l8zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53952.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calotropis gigantea (mudar) / Production host: Escherichia coli (E. coli) References: UniProt: A0A385Z7H9, Transferases; Glycosyltransferases; Hexosyltransferases | ||||
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#2: Chemical | ChemComp-UDP / | ||||
#3: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium chloride, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 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: 2.04→48.44 Å / Num. obs: 28193 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.177 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.04→2.1 Å / Num. unique obs: 2165 / CC1/2: 0.791 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L8Z Resolution: 2.04→48.44 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.93 Å2 / Biso mean: 28.6068 Å2 / Biso min: 13.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→48.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -10.699 Å / Origin y: 6.5865 Å / Origin z: -6.7084 Å
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Refinement TLS group |
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