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- PDB-5x7s: Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x7s | ||||||
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Title | Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase, terbium derivative | ||||||
![]() | Glycoside hydrolase family 31 alpha-glucosidase | ||||||
![]() | HYDROLASE / TRANSFERASE / glydoside hydrolase family 31 / carbohydrate-binding module family 35 / carbohydrate-binding module family 61 | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujimoto, Z. / Kishine, N. / Suzuki, N. / Momma, M. / Ichinose, H. / Kimura, A. / Funane, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Carbohydrate-binding architecture of the multi-modular alpha-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces alpha-1,6-glucosyl-alpha-glucosaccharides from starch Authors: Fujimoto, Z. / Suzuki, N. / Kishine, N. / Ichinose, H. / Momma, M. / Kimura, A. / Funane, K. #1: Journal: Appl. Microbiol. Biotechnol. / Year: 2017 Title: Paenibacillus sp. 598K 6-alpha-glucosyltransferase is essential for cycloisomaltooligosaccharide synthesis from alpha-(1 -> 4)-glucan Authors: Ichinose, H. / Suzuki, R. / Miyazaki, T. / Kimura, K. / Momma, M. / Suzuki, N. / Fujimoto, Z. / Kimura, A. / Funane, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.9 KB | Display | ![]() |
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PDB format | ![]() | 415.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.6 KB | Display | ![]() |
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Full document | ![]() | 504.3 KB | Display | |
Data in XML | ![]() | 92.2 KB | Display | |
Data in CIF | ![]() | 137.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 137684.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A193PKW5, Transferases; Glycosyltransferases; Hexosyltransferases, alpha-glucosidase |
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-Non-polymers , 8 types, 1178 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TB.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-TB / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-MES / #8: Chemical | ChemComp-EDO / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.51 % / Description: Thin parallelogram plate |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 1.5 M magnesium sulfate, 0.1 M MES buffer, 1 mM terbium chloride |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→200 Å / Num. obs: 128840 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.115 / Χ2: 2.045 / Net I/σ(I): 29.4 | ||||||||||||
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6364 / Χ2: 1.109 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.741 Å2
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Refine analyze | Luzzati coordinate error obs: 0.376 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→151.54 Å
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Refine LS restraints |
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