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Yorodumi- PDB-8rw3: Crystal Structure of Agd31B, alpha-transglucosylase, complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rw3 | ||||||
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Title | Crystal Structure of Agd31B, alpha-transglucosylase, complexed with a non-covalent 1,2- Cyclophellitol aziridine | ||||||
Components | Oligosaccharide 4-alpha-D-glucosyltransferase | ||||||
Keywords | STRUCTURAL PROTEIN / Glycoside hydrolase | ||||||
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: 1.9 Å | ||||||
Authors | Moran, E. / Davies, G. / Ofamn, T. / Heming, J. / Nin-Hill, A. / Kullmer, F. / Steneker, R. / Klein, A. / Bennett, M. / Ruijgrok, G. ...Moran, E. / Davies, G. / Ofamn, T. / Heming, J. / Nin-Hill, A. / Kullmer, F. / Steneker, R. / Klein, A. / Bennett, M. / Ruijgrok, G. / Kok, K. / Aerts, J. / Van der Marel, G. / Rovira, C. / Artola, M. / Codee, J. / Overkleeft, H. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Chemistry / Year: 2024 Title: Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining alpha-Glucosidase Inhibition. Authors: Ofman, T.P. / Heming, J.J.A. / Nin-Hill, A. / Kullmer, F. / Moran, E. / Bennett, M. / Steneker, R. / Klein, A.M. / Ruijgrok, G. / Kok, K. / Armstrong, Z.W.B. / Aerts, J.M.F.G. / van der ...Authors: Ofman, T.P. / Heming, J.J.A. / Nin-Hill, A. / Kullmer, F. / Moran, E. / Bennett, M. / Steneker, R. / Klein, A.M. / Ruijgrok, G. / Kok, K. / Armstrong, Z.W.B. / Aerts, J.M.F.G. / van der Marel, G.A. / Rovira, C. / Davies, G.J. / Artola, M. / Codee, J.D.C. / Overkleeft, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rw3.cif.gz | 488.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rw3.ent.gz | 396.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/8rw3 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/8rw3 | HTTPS FTP |
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-Related structure data
Related structure data | 8rvkC C: citing same article (ref.) |
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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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules CAB
#1: Protein | Mass: 92511.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria) 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, 1018 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #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: 3.11 Å3/Da / Density % sol: 60.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 Ammonium sulfate, 0.1 M HEPES pH 7.0, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.83 Å / Num. obs: 270451 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.99 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 13299 / CC1/2: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.517 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.557 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→49.82 Å
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