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Open data
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Basic information
Entry | Database: PDB / ID: 9ju0 | ||||||
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Title | C-terminally truncated dextran dextrinase bound with acarbose | ||||||
![]() | Dextran dextrinase | ||||||
![]() | TRANSFERASE / Glucosyl transferase | ||||||
Function / homology | ![]() dextrin dextranase / dextrin dextranase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tagami, T. / Matsugaki, N. / Saburi, W. / Okuyama, M. / Mori, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of transglucosylation in dextran dextrinase, a homolog of anomer-inverting GH15 glucoside hydrolases. Authors: Tagami, T. / Saburi, W. / Sadahiro, J. / Kumagai, Y. / Lang, W. / Matsugaki, N. / Okuyama, M. / Mori, H. / Kimura, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 726.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 143.9 KB | Display | |
Data in CIF | ![]() | 201.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 98111.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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 #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 10% PEG 6000, 6% Ethylene glycol, 100 mM sodium acetate buffer (pH 3.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.11 Å / Num. obs: 150716 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.99 / Rrim(I) all: 0.252 / Rsym value: 0.236 / Net I/σ(I): 8.64 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 7.6 % / Num. unique obs: 24036 / CC1/2: 0.713 / Rrim(I) all: 1.202 / Rsym value: 1.194 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.858 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→49.106 Å
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Refine LS restraints |
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