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Yorodumi- PDB-7yo7: Bifunctional xylosidase/glucosidase LXYL with intermediate substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yo7 | ||||||
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Title | Bifunctional xylosidase/glucosidase LXYL with intermediate substrate xylose, 5 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: 1.81 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: 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 | 7yo7.cif.gz | 322 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yo7.ent.gz | 264.5 KB | Display | PDB format |
PDBx/mmJSON format | 7yo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yo7 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yo7 | HTTPS FTP |
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-Related structure data
Related structure data | 7ey1C 7ey2C 7yo6C 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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Unit cell |
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Components on special symmetry positions |
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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.) Lentinula edodes (shiitake mushroom) / Gene: Lxyl-p1-2 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: G8GLP2 |
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-Sugars , 5 types, 16 molecules
#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: isolated from a genetically manipulated source | ||||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / #7: Sugar | |
-Non-polymers , 2 types, 975 molecules
#6: Chemical | #8: 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: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 15% PEG3350, 0.1 M Tris-HCl pH8.0, 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: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→73.54 Å / Num. obs: 161417 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / Χ2: 0.97 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.81→1.86 Å / Redundancy: 14 % / Rmerge(I) obs: 1.229 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11837 / CC1/2: 0.794 / Rpim(I) all: 0.495 / Rrim(I) all: 1.325 / Χ2: 0.66 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KJ0 Resolution: 1.81→73.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.946 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.133 / 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: 88.54 Å2 / Biso mean: 35.027 Å2 / Biso min: 20.35 Å2
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Refinement step | Cycle: final / Resolution: 1.81→73.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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