|Entry||Database: PDB / ID: 3d3i|
|Title||Crystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to glycoside hydrolase family 63|
|Components||Uncharacterized protein ygjK|
|Keywords||HYDROLASE / GH63 / processing alpha-glucosidase / alpha/alpha barrel|
|Function / homology|
Function and homology information
glucosidase complex / organic substance catabolic process / alpha,alpha-trehalase activity / trehalose catabolic process / glucosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellular response to DNA damage stimulus / metal ion binding
Similarity search - Function
Ribosomal protein L30p/L7e / putative glycoside hydrolase family protein from bacillus halodurans / Helix Hairpins - #100 / Glycoside hydrolase, family 37 / Trehalase / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Beta-galactosidase; Chain A, domain 5 ...Ribosomal protein L30p/L7e / putative glycoside hydrolase family protein from bacillus halodurans / Helix Hairpins - #100 / Glycoside hydrolase, family 37 / Trehalase / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Escherichia coli (E. coli)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å|
|Authors||Kurakata, Y. / Uechi, A. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.|
Journal: J.Mol.Biol. / Year: 2008
Title: Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.
Authors: Kurakata, Y. / Uechi, A. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.
|Structure viewer||Molecule: |
Downloads & links
A: Uncharacterized protein ygjK
B: Uncharacterized protein ygjK
A: Uncharacterized protein ygjK
B: Uncharacterized protein ygjK
Mass: 86779.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygjK, b3080, JW3051 / Plasmid: pYgjK-SIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42592
|#2: Chemical||#3: Chemical|
|#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 |
Details: 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97912 Å|
|Detector||Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2006|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97912 Å / Relative weight: 1|
|Reflection||Resolution: 1.78→50 Å / Num. obs: 139299|
|Refinement||Method to determine structure: SAD / Resolution: 1.78→50 Å|
|Refinement step||Cycle: LAST / Resolution: 1.78→50 Å|
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