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Yorodumi- PDB-7p4d: Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p4d | |||||||||
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Title | Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130 | |||||||||
Components | Oligosaccharide 4-alpha-D-glucosyltransferase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / GH31 / inhibitor / carbohydrate | |||||||||
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 Ueda107 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Wu, L. / Davies, G.J. | |||||||||
Funding support | European Union, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease. Authors: Kok, K. / Kuo, C.L. / Katzy, R.E. / Lelieveld, L.T. / Wu, L. / Roig-Zamboni, V. / van der Marel, G.A. / Codee, J.D.C. / Sulzenbacher, G. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. / Artola, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p4d.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p4d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p4d_validation.pdf.gz | 937.6 KB | Display | wwPDB validaton report |
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Full document | 7p4d_full_validation.pdf.gz | 944.3 KB | Display | |
Data in XML | 7p4d_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 7p4d_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/7p4d ftp://data.pdbj.org/pub/pdb/validation_reports/p4/7p4d | HTTPS FTP |
-Related structure data
Related structure data | 7p2zC 7p32C 7p4cC 4b9yS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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, 1 molecules AAA
#1: Protein | Mass: 94592.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria) Strain: Ueda107 / Gene: agd31B, CJA_3248 / Production host: Escherichia coli (E. coli) References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase |
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-Non-polymers , 6 types, 498 molecules
#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-OXL / | #5: Chemical | ChemComp-56I / [( | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Jul 19, 2019 |
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→98.54 Å / Num. obs: 99190 / % possible obs: 100 % / Redundancy: 24.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.027 / Rrim(I) all: 0.136 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 2.685 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4849 / CC1/2: 0.696 / Rpim(I) all: 0.545 / Rrim(I) all: 2.741 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4b9y Resolution: 1.85→98.538 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.112 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→98.538 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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