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- PDB-5i23: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i23 | ||||||
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Title | Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF022 | ||||||
![]() | Oligosaccharide 4-alpha-D-glucosyltransferase | ||||||
![]() | TRANSFERASE / Alpha glycosidase / Cyclophellitol Aziridine / Inhibitor / Probe | ||||||
Function / homology | ![]() oligosaccharide 4-alpha-D-glucosyltransferase / oligosaccharide 4-alpha-D-glucosyltransferase activity / alpha-glucosidase activity / N-glycan processing / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, L. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Detection of Active Mammalian GH31 alpha-Glucosidases in Health and Disease Using In-Class, Broad-Spectrum Activity-Based Probes. Authors: Jiang, J. / Kuo, C.L. / Wu, L. / Franke, C. / Kallemeijn, W.W. / Florea, B.I. / van Meel, E. / van der Marel, G.A. / Codee, J.D. / Boot, R.G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.6 KB | Display | ![]() |
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PDB format | ![]() | 272.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 648.7 KB | Display | ![]() |
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Full document | ![]() | 649 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 53.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i24C ![]() 4b9yS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 94592.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: agd31B, CJA_3248 / Production host: ![]() ![]() References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase |
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-Non-polymers , 5 types, 641 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/66V.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/66V.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PG4 / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-66V / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→171.47 Å / Num. obs: 86417 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 0.801 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4B9Y Resolution: 1.95→171.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.014 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / 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: 35.753 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→171.47 Å
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Refine LS restraints |
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