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- PDB-5yif: Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yif | ||||||
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Title | Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, E163A mutant pyruvylated beta-D-galactose complex | ||||||
![]() | Pyruvylated beta-D-galactosidase | ||||||
![]() | HYDROLASE / glycoside hydrolase | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanuma, M. / Yamada, C. / Arakawa, T. / Higuchi, Y. / Takegawa, K. / Fushinobu, S. | ||||||
![]() | ![]() Title: Identification and characterization of a novel beta-D-galactosidase that releases pyruvylated galactose. Authors: Higuchi, Y. / Matsufuji, H. / Tanuma, M. / Arakawa, T. / Mori, K. / Yamada, C. / Shofia, R. / Matsunaga, E. / Tashiro, K. / Fushinobu, S. / Takegawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200 KB | Display | ![]() |
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PDB format | ![]() | 158.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yhsSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 55494.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 32% PEG 300, 0.1 M phosphate-citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2017 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→100 Å / Num. obs: 42682 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 45.897 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2129 / CC1/2: 0.621 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YHS Resolution: 2.45→99.4 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.102 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.295 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.497 Å2
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Refine analyze | Luzzati coordinate error obs: 0.244 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.45→99.4 Å
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Refine LS restraints |
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