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Yorodumi- PDB-3w7w: Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w7w | |||||||||
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Title | Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-D-glucopyranosyl-alpha-D-galactopyranose | |||||||||
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 / 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: 2 Å | |||||||||
Authors | Miyazaki, T. / Ichikawa, M. / Yokoi, G. / Kitaoka, M. / Mori, H. / Kitano, Y. / Nishikawa, A. / Tonozuka, T. | |||||||||
Citation | Journal: Febs J. / Year: 2013 Title: Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity. Authors: Miyazaki, T. / Ichikawa, M. / Yokoi, G. / Kitaoka, M. / Mori, H. / Kitano, 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 | 3w7w.cif.gz | 328.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w7w.ent.gz | 262.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w7w_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3w7w_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3w7w_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 3w7w_validation.cif.gz | 87.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/3w7w ftp://data.pdbj.org/pub/pdb/validation_reports/w7/3w7w | HTTPS FTP |
-Related structure data
Related structure data | 3w7xC 3c68 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 85946.781 Da / Num. of mol.: 2 / Mutation: E727A 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: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-MG / #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: 1.93 Å3/Da / Density % sol: 36.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 13, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 86824 / % possible obs: 100 % / Rmerge(I) obs: 0.103 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C68 3c68 Resolution: 2→31.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.768 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.184 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.911 Å2
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Refinement step | Cycle: LAST / Resolution: 2→31.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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