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Yorodumi- PDB-7cwd: Crystal structure of beta-galactosidase II from Bacillus circulan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cwd | ||||||
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Title | Crystal structure of beta-galactosidase II from Bacillus circulans in complex with beta-D-galactopyranosyl disaccharide | ||||||
Components | beta-glalactosidase | ||||||
Keywords | HYDROLASE / beta-galactosidase / CARBOHYDRATE | ||||||
Function / homology | Function and homology information beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hong, H. / Seo, H. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2020 Title: High Galacto-Oligosaccharide Production and a Structural Model for Transgalactosylation of beta-Galactosidase II from Bacillus circulans . Authors: Choi, J.Y. / Hong, H. / Seo, H. / Pan, J.G. / Kim, E.J. / Maeng, P.J. / Yang, T.H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cwd.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cwd.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cwd_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7cwd_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7cwd_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 7cwd_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/7cwd ftp://data.pdbj.org/pub/pdb/validation_reports/cw/7cwd | HTTPS FTP |
-Related structure data
Related structure data | 7cwiC 4ypjS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 91860.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M5K904*PLUS, beta-galactosidase | ||||||||
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#2: Sugar | ChemComp-GLC / | ||||||||
#3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | GLC A 901 and GAL A 903 existed in alternate conformations in this structure. | Sequence details | THE SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION NUMBER QJU69416. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Ammonium sulfate, Sodium acetate, Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 89811 / % possible obs: 94.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Χ2: 2.066 / Net I/σ(I): 11.4 / Num. measured all: 497629 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPJ Resolution: 2→33.28 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 106.34 Å2 / Biso mean: 29.9466 Å2 / Biso min: 8.91 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.28 Å
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LS refinement shell | Resolution: 2→2.03 Å |