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- PDB-1ug9: Crystal Structure of Glucodextranase from Arthrobacter globiformis I42 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ug9 | ||||||
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Title | Crystal Structure of Glucodextranase from Arthrobacter globiformis I42 | ||||||
![]() | glucodextranase | ||||||
![]() | HYDROLASE / alpha-alpha-six-barrels / GH Family 15 | ||||||
Function / homology | ![]() glucan 1,4-alpha-glucosidase activity / glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Ohtaki, A. / Kamitori, S. / Nishikawa, A. / Sakano, Y. | ||||||
![]() | ![]() Title: Structural insights into substrate specificity and function of glucodextranase Authors: Mizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Kamitori, S. / Nishikawa, A. / Sakano, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.9 KB | Display | ![]() |
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PDB format | ![]() | 164.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 478.8 KB | Display | |
Data in XML | ![]() | 44.4 KB | Display | |
Data in CIF | ![]() | 64.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ulvC ![]() 1lf6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 106526.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2003 |
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→19.881 Å / Num. all: 45620 / Num. obs: 45620 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.216 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 50 Å / Num. obs: 48376 / % possible obs: 96 % / Num. measured all: 193427 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 2.51 Å / % possible obs: 62.1 % / Rmerge(I) obs: 0.223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LF6 Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4085992.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.0677 Å2 / ksol: 0.321673 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 19.9 Å / Num. reflection obs: 48379 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 2.51 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.254 |