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Yorodumi- PDB-5npd: Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5npd | ||||||
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Title | Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Aziridine probe CF021 | ||||||
Components | Oligosaccharide 4-alpha-D-glucosyltransferase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information oligosaccharide 4-alpha-D-glucosyltransferase / oligosaccharide 4-alpha-D-glucosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Cellvibrio japonicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wu, L. / Davies, G.J. | ||||||
Citation | Journal: ACS Cent Sci / Year: 2017 Title: 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. Authors: Artola, M. / Wu, L. / Ferraz, M.J. / Kuo, C.L. / Raich, L. / Breen, I.Z. / Offen, W.A. / Codee, J.D.C. / van der Marel, G.A. / Rovira, C. / Aerts, J.M.F.G. / Davies, G.J. / 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 | 5npd.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5npd.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 5npd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5npd_validation.pdf.gz | 498.6 KB | Display | wwPDB validaton report |
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Full document | 5npd_full_validation.pdf.gz | 501.5 KB | Display | |
Data in XML | 5npd_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 5npd_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/5npd ftp://data.pdbj.org/pub/pdb/validation_reports/np/5npd | HTTPS FTP |
-Related structure data
Related structure data | 5npbC 5npcC 5npeC 5npfC 5o0sC 4b9yS C: citing same article (ref.) S: Starting model for refinement |
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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: 94460.523 Da / Num. of mol.: 1 / Mutation: D412N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellvibrio japonicus (bacteria) / 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, 508 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PG4 / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-94B / ( | #6: Chemical | ChemComp-OXL / | #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: 59.76 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 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: 1.95→47.39 Å / Num. obs: 85623 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.023 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.408 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4474 / CC1/2: 0.899 / Rpim(I) all: 0.32 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4b9y Resolution: 1.95→47.39 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.356 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / 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: 36.926 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→47.39 Å
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Refine LS restraints |
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