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- PDB-7ey1: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ey1 | |||||||||
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Title | Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose | |||||||||
![]() | 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 | ![]() ![]() ![]() | |||||||||
![]() | Gong, W.M. / Yang, L.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose Authors: Gong, W.M. / 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 | ![]() | 607 KB | Display | ![]() |
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PDB format | ![]() | 499.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.2 MB | Display | ![]() |
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Full document | ![]() | 5.3 MB | Display | |
Data in XML | ![]() | 117.2 KB | Display | |
Data in CIF | ![]() | 162.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ey2C ![]() 7yo6C ![]() 7yo7C ![]() 8gyyC ![]() 6kj0S 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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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 86036.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 11 types, 38 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/XYP.gif)
![](data/chem/img/XYZ.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/XYP.gif)
![](data/chem/img/XYZ.gif)
![](data/chem/img/MAN.gif)
![](data/chem/img/BMA.gif)
#2: Polysaccharide | Type: oligosaccharide / Mass: 1356.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(4-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(4-3)-alpha-D-mannopyranose-(1-4)-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: isolated from a genetically manipulated source #4: Polysaccharide | #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1 / Source method: obtained synthetically #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(6-4)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1 / Source method: obtained synthetically #7: Polysaccharide | alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose | #8: Sugar | ChemComp-NAG / #10: Sugar | ChemComp-XYP / | #11: Sugar | ChemComp-XYZ / | #12: Sugar | ChemComp-MAN / | #13: Sugar | ChemComp-BMA / | |
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-Non-polymers , 2 types, 737 molecules ![](data/chem/img/BKR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | #14: 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: 3.2 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 3350, 0.1M Hepes pH 7.5, 0.2% MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→218.5 Å / Num. obs: 158265 / % possible obs: 98.74 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.46→2.5 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 7844 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KJ0 Resolution: 2.46→218.5 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.46→218.5 Å
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