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Yorodumi- PDB-7dch: Alpha-glucosidase from Weissella cibaria BBK-1 bound with acarbose -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dch | ||||||
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Title | Alpha-glucosidase from Weissella cibaria BBK-1 bound with acarbose | ||||||
Components | Alpha-glycosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism / CARBOHYDRATE | ||||||
Biological species | Weissella cibaria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.692 Å | ||||||
Authors | Krusong, K. / Wangpaiboon, K. / Kim, S. / Mori, T. / Hakoshima, T. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: A GH13 alpha-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. Authors: Wangpaiboon, K. / Laohawuttichai, P. / Kim, S.Y. / Mori, T. / Nakapong, S. / Pichyangkura, R. / Pongsawasdi, P. / Hakoshima, T. / Krusong, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dch.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dch.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dch_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7dch_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7dch_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 7dch_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/7dch ftp://data.pdbj.org/pub/pdb/validation_reports/dc/7dch | HTTPS FTP |
-Related structure data
Related structure data | 7d9bSC 7d9cC 7dcgC 7ehhC 7ehiC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 68398.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Weissella cibaria (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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#2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 546 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, dioxane, MES |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2019 |
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: 76028 / % possible obs: 91.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.31 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 21.244 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 3.2 % / Num. unique obs: 15816 / Rpim(I) all: 0.416 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D9B Resolution: 1.692→27.755 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 26.25 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.692→27.755 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.692→1.7136 Å
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