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Yorodumi- PDB-7ey1: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ey1 | |||||||||
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Title | Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose | |||||||||
Components | Beta-D-xylosidase/beta-D-glucosidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolases / xylosidases / bifunctional | |||||||||
Function / homology | Function and homology information glucan catabolic process / beta-glucosidase / beta-glucosidase activity / extracellular region Similarity search - Function | |||||||||
Biological species | Lentinula edodes (shiitake mushroom) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | |||||||||
Authors | Gong, W.M. / Yang, L.Y. | |||||||||
Funding support | China, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ey1.cif.gz | 607 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ey1.ent.gz | 499.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ey1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ey1_validation.pdf.gz | 5.2 MB | Display | wwPDB validaton report |
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Full document | 7ey1_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 7ey1_validation.xml.gz | 117.2 KB | Display | |
Data in CIF | 7ey1_validation.cif.gz | 162.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/7ey1 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/7ey1 | HTTPS FTP |
-Related structure data
Related structure data | 7ey2C 7yo6C 7yo7C 8gyyC 6kj0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Lentinula edodes (shiitake mushroom) / Gene: Lxyl-p1-2 / Production host: Escherichia phage Ecwhy_1 (virus) / References: UniProt: G8GLP2 |
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-Sugars , 11 types, 38 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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