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Yorodumi- PDB-5i24: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i24 | ||||||
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Title | Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF021 | ||||||
Components | Oligosaccharide 4-alpha-D-glucosyltransferase | ||||||
Keywords | HYDROLASE / Alpha glycosidase / Cyclophellitol Aziridine / Inhibitor / Probe | ||||||
Function / homology | Function and homology information 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 | Cellvibrio japonicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Wu, L. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i24.cif.gz | 338.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i24.ent.gz | 273.5 KB | Display | PDB format |
PDBx/mmJSON format | 5i24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/5i24 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/5i24 | HTTPS FTP |
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-Related structure data
Related structure data | 5i23C 4b9yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Cellvibrio japonicus (strain Ueda107) (bacteria) Strain: Ueda107 / Gene: agd31B, CJA_3248 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase |
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-Non-polymers , 6 types, 646 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-66U / ( | #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: 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: 3.06 Å3/Da / Density % sol: 59.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH7.0), 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→170.87 Å / Num. obs: 100134 / % possible obs: 100 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 25 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B9Y Resolution: 1.85→170.87 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.753 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.096 / 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: 34.16 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→170.87 Å
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Refine LS restraints |
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