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Yorodumi- PDB-8gyy: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gyy | |||||||||
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Title | Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 120 seconds | |||||||||
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: 2.07 Å | |||||||||
Authors | 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: 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 | 8gyy.cif.gz | 626.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gyy.ent.gz | 515.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/8gyy ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gyy | HTTPS FTP |
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-Related structure data
Related structure data | 7ey1C 7ey2C 7yo6C 7yo7C 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules BACD
#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 coli (E. coli) / References: UniProt: G8GLP2 |
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-Sugars , 10 types, 58 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #4: Polysaccharide | beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose | #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: Polysaccharide | alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-1-deoxy-alpha-D-mannopyranose-(1-4)-2- ...alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-1-deoxy-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1 / Source method: obtained synthetically #7: Polysaccharide | #9: Sugar | #10: Sugar | ChemComp-MAN / #11: Sugar | ChemComp-NAG / #12: Sugar | ChemComp-BMA / | |
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-Non-polymers , 2 types, 1298 molecules
#8: Chemical | ChemComp-BKR / #13: 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: 3.43 Å3/Da / Density % sol: 64.13 % |
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Crystal grow | Temperature: 289.16 K / Method: vapor diffusion, sitting drop / Details: 13% PEG3350, 0.1 M Tris-HCl pH8.5, 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: BL18U1 / 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: 2.068→158.24 Å / Num. obs: 257788 / % possible obs: 95.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.067 / Rrim(I) all: 0.132 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.068→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.913 / Num. unique obs: 12570 / CC1/2: 0.584 / Rpim(I) all: 0.555 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KJ0 Resolution: 2.07→35.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.92 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.556 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→35.97 Å
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Refine LS restraints |
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