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Yorodumi- PDB-5ca3: Crystal structure of the glycosynthase mutant D324N of Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ca3 | |||||||||
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Title | Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase in complex with glucose and lactose | |||||||||
Components | Glucosidase YgjK | |||||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH63 / 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: 1.8 Å | |||||||||
Authors | Miyazaki, T. / Tonozuka, T. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: Crystal structure of the enzyme-product complex reveals sugar ring distortion during catalysis by family 63 inverting alpha-glycosidase. Authors: Miyazaki, T. / 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 | 5ca3.cif.gz | 340.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ca3.ent.gz | 270.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ca3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ca3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5ca3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5ca3_validation.xml.gz | 63.6 KB | Display | |
Data in CIF | 5ca3_validation.cif.gz | 96.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/5ca3 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/5ca3 | HTTPS FTP |
-Related structure data
Related structure data | 5gw7C 3w7tS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 86003.836 Da / Num. of mol.: 2 / Mutation: D324N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ygjK, b3080, JW3051 / Plasmid: pYgjK-SIG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P42592, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | #5: Sugar | ChemComp-BGC / | #6: Sugar | ChemComp-GLC / | |
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-Non-polymers , 3 types, 1291 molecules
#3: Chemical | #4: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 8000, 0.4 M magnesium chloride, 100 mM Tris-HCl buffer, pH 6.0 |
-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 210 / Detector: CCD / Date: Nov 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 110133 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 7.2 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W7T Resolution: 1.8→31.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.125 / 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: 15.734 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→31.12 Å
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Refine LS restraints |
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