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- PDB-5npc: Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-tra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5npc | ||||||
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Title | Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with unreacted alpha Cyclophellitol Cyclosulfate probe ME647 | ||||||
![]() | Oligosaccharide 4-alpha-D-glucosyltransferase | ||||||
![]() | HYDROLASE | ||||||
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. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.1 KB | Display | ![]() |
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PDB format | ![]() | 142.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 915.3 KB | Display | ![]() |
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Full document | ![]() | 916.9 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 48 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5npbC ![]() 5npdC ![]() 5npeC ![]() 5npfC ![]() 5o0sC ![]() 4b9yS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: B3PEE6, oligosaccharide 4-alpha-D-glucosyltransferase |
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-Non-polymers , 6 types, 385 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/94E.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/94E.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-94E / ( | #6: Chemical | ChemComp-OXL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion 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: May 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→65.67 Å / Num. obs: 84174 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.046 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 19.2 % / Rmerge(I) obs: 2.991 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6171 / CC1/2: 0.625 / Rpim(I) all: 0.698 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4b9y Resolution: 1.96→65.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.825 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.131 / 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: 38.436 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→65.67 Å
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