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- PDB-1xsk: Structure of a Family 31 alpha glycosidase glycosyl-enzyme interm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xsk | |||||||||
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Title | Structure of a Family 31 alpha glycosidase glycosyl-enzyme intermediate | |||||||||
![]() | Putative family 31 glucosidase yicI | |||||||||
![]() | HYDROLASE / beta(8)alpha(8) barrel and beta sandwich domains | |||||||||
Function / homology | ![]() xyloglucan 1,6-alpha-xylosidase activity / alpha-D-xyloside xylohydrolase / alpha-D-xyloside xylohydrolase / carbohydrate binding / carbohydrate metabolic process / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lovering, A.L. / Lee, S.S. / Kim, Y.W. / Withers, S.G. / Strynadka, N.C. | |||||||||
![]() | ![]() Title: Mechanistic and Structural Analysis of a Family 31 {alpha}-Glycosidase and Its Glycosyl-enzyme Intermediate Authors: Lovering, A.L. / Lee, S.S. / Kim, Y.W. / Withers, S.G. / Strynadka, N.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 908 KB | Display | ![]() |
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PDB format | ![]() | 753.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 552 KB | Display | ![]() |
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Full document | ![]() | 688.3 KB | Display | |
Data in XML | ![]() | 176.2 KB | Display | |
Data in CIF | ![]() | 237.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xsiSC ![]() 1xsjC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 89002.023 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P31434, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-SO4 / #3: Sugar | ChemComp-XYF / #4: Chemical | ChemComp-MPO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium acetate, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 303936 / Num. obs: 296995 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.406 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1XSI Resolution: 2.2→29.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5562235.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4018 Å2 / ksol: 0.354166 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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