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- PDB-5awp: Arthrobacter globiformis T6 isomalto-dextranase complexed with is... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5awp | |||||||||
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Title | Arthrobacter globiformis T6 isomalto-dextranase complexed with isomaltose | |||||||||
![]() | Isomaltodextranase | |||||||||
![]() | HYDROLASE / TIM barrel / glycoside hydrolase / GH27 / carbohydrate binding module / CBM35 | |||||||||
Function / homology | ![]() alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / carbohydrate binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tonozuka, T. | |||||||||
![]() | ![]() Title: Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27 Authors: Okazawa, Y. / Miyazaki, T. / Yokoi, G. / Ishizaki, Y. / Nishikawa, A. / Tonozuka, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.3 KB | Display | ![]() |
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PDB format | ![]() | 109.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5awoSC ![]() 5awqC 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: 66893.109 Da / Num. of mol.: 1 / Fragment: UNP residues 31-636 Source method: isolated from a genetically manipulated source Details: The sequence for the mature enzyme "ATAV ... ELDM" (606 amino acid residues) was fused with N-terminal His-tag, and the expressed protein was digested with thrombin. Therefore, the first ...Details: The sequence for the mature enzyme "ATAV ... ELDM" (606 amino acid residues) was fused with N-terminal His-tag, and the expressed protein was digested with thrombin. Therefore, the first four N-terminal residues GSHM are derived from the expression plasmid pET28a. Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: PEG 8000, sodium acetate buffer, potassium dihydrogenphosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 43201 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 40 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 13.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AWO Resolution: 2→30.45 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.31 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.836 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30.45 Å
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Refine LS restraints |
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