+Open data
-Basic information
Entry | Database: PDB / ID: 8cgq | ||||||
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Title | Crystal structure of UGT708A6 with UDP | ||||||
Components | UDP-glycosyltransferase 708A6 | ||||||
Keywords | TRANSFERASE / Enzyme GT-B GT1 | ||||||
Function / homology | flavanone 7-O-beta-glucosyltransferase activity / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 708A6 Function and homology information | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Fredslund, F. / Bidart, G.N. / Welner, D.H. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: To Be Published Title: Crystal structure of UGT708A6 with UDP Authors: Fredslund, F. / Bidart, G.N. / Welner, D.H. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. #2: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cgq.cif.gz | 315 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cgq.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cgq ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cgq | 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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Unit cell |
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-Components
#1: Protein | Mass: 50720.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: UGT708A6 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A096SRM5, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-UDP / |
#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: 2.05 Å3/Da / Density % sol: 40.15 % / Description: Long rods, with crevice in the middle |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350 20% w/v, BIS-TRIS propane 100mM, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→44.26 Å / Num. obs: 25283 / % possible obs: 96.73 % / Observed criterion σ(F): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1077 / Rpim(I) all: 0.04557 / Rrim(I) all: 0.1171 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.04→2.12 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.9246 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 2028 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.51 / Rrim(I) all: 1.063 / % possible all: 77.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→44.26 Å / SU ML: 0.2785 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.596 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: 46.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→44.26 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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