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- PDB-7yo6: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yo6 | ||||||
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Title | Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose for 5 sec | ||||||
![]() | Beta-D-xylosidase/beta-D-glucosidase | ||||||
![]() | HYDROLASE / glycoside hydrolases / xylosidases / bifunctional | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, L.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose Authors: Yang, L.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315.1 KB | Display | ![]() |
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PDB format | ![]() | 259.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 63.9 KB | Display | |
Data in CIF | ![]() | 90.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ey1SC ![]() 7ey2C ![]() 7yo7C ![]() 8gyyC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 86036.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 6 types, 16 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/XYZ.gif)
![](data/chem/img/XYL.gif)
![](data/chem/img/XYZ.gif)
![](data/chem/img/XYL.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-1)-alpha-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-1)-alpha-D-mannopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 789.734 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: Polysaccharide | Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically #5: Sugar | ChemComp-NAG / #7: Sugar | ChemComp-XYZ / | #8: Sugar | ChemComp-XYL / | |
-Non-polymers , 2 types, 733 molecules ![](data/chem/img/BKR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 15% PEG3350, pH 8.0 Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.539→200 Å / Num. obs: 57972 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.976 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.539→2.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2855 / CC1/2: 0.937 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EY1 Resolution: 2.54→120.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.74 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.815 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 104.67 Å2 / Biso mean: 33.39 Å2 / Biso min: 11.28 Å2
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Refinement step | Cycle: final / Resolution: 2.54→120.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.605 Å / Rfactor Rfree error: 0
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