+Open data
-Basic information
Entry | Database: PDB / ID: 3w7t | |||||||||
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Title | Escherichia coli K12 YgjK complexed with mannose | |||||||||
Components | Uncharacterized protein YgjK | |||||||||
Keywords | HYDROLASE / GH63 / processing alpha-glucosidase I / alpha/alpha barrel | |||||||||
Function / homology | Function and homology information glucosidase complex / trehalose catabolic process / alpha,alpha-trehalase activity / glucosidase activity / organic substance catabolic process / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Miyazaki, T. / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w7t.cif.gz | 347.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w7t.ent.gz | 281 KB | Display | PDB format |
PDBx/mmJSON format | 3w7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/3w7t ftp://data.pdbj.org/pub/pdb/validation_reports/w7/3w7t | HTTPS FTP |
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-Related structure data
Related structure data | 3d3iC 3w7sC 3w7uC 2ds3 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 86004.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3080, JW3051, ygjK / Plasmid: pYgjK-SIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42592 #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-BMA / #5: 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: 42.64 % |
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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, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 222770 / % possible obs: 96.6 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.93 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DS3 2ds3 Resolution: 1.5→46.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.185 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.792 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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