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Yorodumi- PDB-8ibk: Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ibk | ||||||
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Title | Crystal structure of Bacillus sp. AHU2216 GH13_31 Alpha-glucosidase E256Q/N258G in complex with maltotriose | ||||||
Components | Alpha-glucosidase | ||||||
Keywords | HYDROLASE / alpha-glucosidase / GH13_31 / complex / alpha-amylase | ||||||
Function / homology | Function and homology information oligosaccharide catabolic process / alpha-amylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Auiewiriyanukul, W. / Saburi, W. / Yu, J. / Kato, K. / Yao, M. / Mori, H. | ||||||
Funding support | 1items
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Citation | Journal: Molecules / Year: 2023 Title: Alteration of Substrate Specificity and Transglucosylation Activity of GH13_31 alpha-Glucosidase from Bacillus sp. AHU2216 through Site-Directed Mutagenesis of Asn258 on beta → alpha Loop 5. Authors: Auiewiriyanukul, W. / Saburi, W. / Ota, T. / Yu, J. / Kato, K. / Yao, M. / Mori, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ibk.cif.gz | 141.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ibk.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ibk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8ibk ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ibk | HTTPS FTP |
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-Related structure data
Related structure data | 8idsC 5zcdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65942.562 Da / Num. of mol.: 1 / Mutation: E256Q,N258G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (in: firmicutes) (bacteria) Gene: BspAG13A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5WH92 | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 mM G3, 0.2 M CaCl2, and 20% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. obs: 72935 / % possible obs: 99.6 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 17.22 |
Reflection shell | Resolution: 1.69→1.8 Å / Mean I/σ(I) obs: 1.99 / Num. unique obs: 11510 / CC1/2: 0.864 / Rrim(I) all: 0.981 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZCD Resolution: 1.69→47.98 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→47.98 Å
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Refine LS restraints |
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LS refinement shell |
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