+Open data
-Basic information
Entry | Database: PDB / ID: 7w09 | ||||||||||||
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Title | UGT74AN2, Plant Steroid Glycosyltransferase | ||||||||||||
Components | Glycosyltransferase | ||||||||||||
Keywords | TRANSFERASE / Apo / UGT74AN2 / Glycosyltransferase | ||||||||||||
Function / homology | UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / hexosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / Glycosyltransferase Function and homology information | ||||||||||||
Biological species | Calotropis gigantea (mudar) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 7w09.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w09.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 7w09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/7w09 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/7w09 | HTTPS FTP |
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-Related structure data
Related structure data | 7w0kC 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: A0A385Z7H9, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.77 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium chloride, MES (pH 6.5) |
-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: 1.95→49.77 Å / Num. obs: 32926 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2268 / CC1/2: 0.866 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L8Z Resolution: 1.95→30.4 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6729 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: 26.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→30.4 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: -10.6804716418 Å / Origin y: 7.79397863673 Å / Origin z: -6.8032148354 Å
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Refinement TLS group | Selection details: all |