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Yorodumi- PDB-3d3i: Crystal structural of Escherichia coli K12 YgjK, a glucosidase be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d3i | |||||||||
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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 / trehalose catabolic process / alpha,alpha-trehalase activity / : / glucosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / DNA damage response / metal ion binding Similarity search - Function | |||||||||
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. | |||||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray analysis of Escherichia coli K12 YgjK protein, a member of glycosyl hydrolase family 63 Authors: Tonozuka, T. / Uechi, A. / Mizuno, M. / Ichikawa, K. / Nishikawa, A. / Sakano, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d3i.cif.gz | 349.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d3i.ent.gz | 290.5 KB | Display | PDB format |
PDBx/mmJSON format | 3d3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d3i_validation.pdf.gz | 449.3 KB | Display | wwPDB validaton report |
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Full document | 3d3i_full_validation.pdf.gz | 475.8 KB | Display | |
Data in XML | 3d3i_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 3d3i_validation.cif.gz | 114.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3i ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | 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 | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→50 Å
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Refinement step | Cycle: LAST / Resolution: 1.78→50 Å
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