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Yorodumi- PDB-8puo: Structural determinants of cold-activity and glucose tolerance of... -
+Open data
-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 | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / cold-active enzymes / GH1 family / psychrophiles / glucose-tolerance | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Marinomonas sp. ef1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Gourlay, L.J. / Nardini, M. | ||||||
Funding support | 1items
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Citation | Journal: Febs J. / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8puo.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8puo.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 8puo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/8puo ftp://data.pdbj.org/pub/pdb/validation_reports/pu/8puo | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-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.) Marinomonas sp. ef1 (bacteria) / Gene: TY87_18135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M8K1U8, beta-glucosidase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
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: 0.9677 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.88 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.98 / Stereochemistry target values: ML
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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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