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Yorodumi- PDB-8i8z: Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i8z | ||||||
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Title | Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from Nemophila menziesii, apo form | ||||||
Components | Glycosyltransferase | ||||||
Keywords | PLANT PROTEIN / flavone | ||||||
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 | Nemophila menziesii (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
Funding support | 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2024 Title: Molecular basis of ligand recognition specificity of flavone glucosyltransferases in Nemophila menziesii. Authors: Murayama, K. / Kato-Murayama, M. / Hosaka, T. / Okitsu, N. / Tanaka, Y. / Shirouzu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i8z.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i8z.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/8i8z ftp://data.pdbj.org/pub/pdb/validation_reports/i8/8i8z | HTTPS FTP |
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-Related structure data
Related structure data | 8i90C 8i94C 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: 54380.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nemophila menziesii (plant) / Gene: NmF4'G7GT / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: A0A292GEP7, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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: 45.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Tris-HCl, Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.38 Å / Num. obs: 20008 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.69 Å2 / Rrim(I) all: 0.153 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 1920 / CC1/2: 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.38 Å / SU ML: 0.293 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.6802 / Stereochemistry target values: GeoStd + Monomer Library
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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: 46.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.38 Å
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Refine LS restraints |
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LS refinement shell |
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