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Yorodumi- PDB-7d9c: Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltose -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d9c | ||||||
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Title | Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltose | ||||||
Components | Alpha-glycosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism | ||||||
Function / homology | alpha-maltose / beta-D-glucopyranose / alpha-D-glucopyranose Function and homology information | ||||||
Biological species | Weissella confusa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 | 7d9c.cif.gz | 311.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d9c.ent.gz | 219.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d9c_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7d9c_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7d9c_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 7d9c_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/7d9c ftp://data.pdbj.org/pub/pdb/validation_reports/d9/7d9c | HTTPS FTP |
-Related structure data
Related structure data | 7d9bSC 7dcgC 7dchC 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 , 1 types, 1 molecules A
#1: Protein | Mass: 68398.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Weissella confusa (bacteria) / Gene: C6P08_07940 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: alpha-glucosidase |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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#6: Sugar | ChemComp-GLC / |
#7: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 623 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG_256496 FOR THE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.51 % |
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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: Mar 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 152899 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.46 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 48.34 |
Reflection shell | Resolution: 1.36→1.41 Å / Num. unique obs: 15113 / Rpim(I) all: 0.358 / Rrim(I) all: 0.946 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D9B Resolution: 1.36→26.76 Å / SU ML: 0.1112 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.1479 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→26.76 Å
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Refine LS restraints |
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LS refinement shell |
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