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Yorodumi- PDB-5yhs: Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, apo form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yhs | ||||||
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Title | Pyruvylated beta-D-galactosidase from Bacillus sp. HMA207, apo form | ||||||
Components | Pyruvylated beta-D-galactosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Tanuma, M. / Yamada, C. / Arakawa, T. / Higuchi, Y. / Takegawa, K. / Fushinobu, S. | ||||||
Citation | Journal: Sci Rep / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yhs.cif.gz | 191.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yhs.ent.gz | 151.8 KB | Display | PDB format |
PDBx/mmJSON format | 5yhs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yhs_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 5yhs_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 5yhs_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 5yhs_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/5yhs ftp://data.pdbj.org/pub/pdb/validation_reports/yh/5yhs | HTTPS FTP |
-Related structure data
Related structure data | 5yifC 3ta9S 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
#1: Protein | Mass: 55552.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: HMA207 / Gene: ORF1119 / Plasmid: pET32b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): codon plus RIL / References: UniProt: A0A2B9BPQ7*PLUS #2: 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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: Hexagonal plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 50% PEG300, 0.1M phosphate-citrate buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 2016 |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 39354 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 56.122 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1925 / CC1/2: 0.777 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TA9 Resolution: 2.5→98.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.716 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.314 / 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: 56.492 Å2
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Refine analyze | Luzzati coordinate error obs: 0.292 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.5→98.72 Å
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Refine LS restraints |
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