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- PDB-8puo: Structural determinants of cold-activity and glucose tolerance of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8puo | ||||||
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Title | Structural determinants of cold-activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas Ef 1 | ||||||
![]() | Beta-glucosidase![]() | ||||||
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Function / homology | ![]() scopolin beta-glucosidase activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gourlay, L.J. / Nardini, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural determinants of cold activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas sp. ef1. Authors: Gourlay, L.J. / Mangiagalli, M. / Moroni, E. / Lotti, M. / Nardini, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.5 KB | Display | ![]() |
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PDB format | ![]() | 158.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
#1: Protein | ![]() Mass: 51814.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: M-GH1 crystals grew over 2-4 days in 50% protein drop in an optimized condition of PACT condition G1, containing 22% (w/v) PEG 3500, 0.1 M sodium fluoride (NaF) and 0.1 M Tris-HCl pH 8.5. |
-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: Oct 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→67 Å / Num. obs: 91533 / % possible obs: 98.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 20.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12892 / CC1/2: 0.805 / Rrim(I) all: 1.038 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.88 Å
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Refine LS restraints |
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LS refinement shell |
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