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Yorodumi- PDB-5x7s: Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x7s | ||||||
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Title | Crystal structure of Paenibacillus sp. 598K alpha-1,6-glucosyltransferase, terbium derivative | ||||||
Components | Glycoside hydrolase family 31 alpha-glucosidase | ||||||
Keywords | HYDROLASE / TRANSFERASE / glydoside hydrolase family 31 / carbohydrate-binding module family 35 / carbohydrate-binding module family 61 | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Paenibacillus sp. 598K (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Fujimoto, Z. / Kishine, N. / Suzuki, N. / Momma, M. / Ichinose, H. / Kimura, A. / Funane, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem. J. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x7s.cif.gz | 526.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x7s.ent.gz | 415.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/5x7s ftp://data.pdbj.org/pub/pdb/validation_reports/x7/5x7s | HTTPS FTP |
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-Related 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, 2 molecules AB
#1: Protein | Mass: 137684.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. 598K (bacteria) / Strain: 598K / Gene: 6gt31a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A193PKW5, Transferases; Glycosyltransferases; Hexosyltransferases, alpha-glucosidase |
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-Non-polymers , 8 types, 1178 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.64883,1.64955,1.60679 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→151.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.743 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.255 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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