+Open data
-Basic information
Entry | Database: PDB / ID: 3hbf | ||||||
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Title | Structure of UGT78G1 complexed with myricetin and UDP | ||||||
Components | Flavonoid 3-O-glucosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / GT-B fold / GT1 / Phenylpropanoid metabolism | ||||||
Function / homology | Function and homology information phenylpropanoid metabolic process / flavonoid biosynthetic process / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wang, X. / Modolo, L. / Li, L. / Dixon, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structures of glycosyltransferase UGT78G1 reveal the molecular basis for glycosylation and deglycosylation of (iso)flavonoids. Authors: Modolo, L.V. / Li, L. / Pan, H. / Blount, J.W. / Dixon, R.A. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hbf.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hbf.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hbf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3hbf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3hbf_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 3hbf_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/3hbf ftp://data.pdbj.org/pub/pdb/validation_reports/hb/3hbf | HTTPS FTP |
-Related 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: 50215.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: GT83F, UGT78G1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A6XNC6, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-MYC / |
#4: 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: 2.25 Å3/Da / Density % sol: 45.29 % |
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Crystal grow | Temperature: 290 K / pH: 5.5 Details: 25% PEG 3350, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 290K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.82 Å / Num. obs: 25599 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.6 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.82 Å / Rfactor Rfree error: 0.005 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→35.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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