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Yorodumi- PDB-8i0x: Beta-Xylosidase JB13GH39P28 showing salt/ethanol/trypsin toleranc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i0x | ||||||
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Title | Beta-Xylosidase JB13GH39P28 showing salt/ethanol/trypsin tolerance, low-pH/low-Temperature activity, and transformation of notoginsenosides | ||||||
Components | Glycoside hydrolase family 39 beta-xylosidase | ||||||
Keywords | HYDROLASE / salt tolerance / transformation of notoginsenosides | ||||||
Function / homology | : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glycoside hydrolase family 39 beta-xylosidase Function and homology information | ||||||
Biological species | Sphingomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhou, J.P. / Cao, L.J. / Lin, M.Y. / Zhang, R. / Huang, Z.X. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: beta-Xylosidase JB13GH39P28(D41G)showing salt/ethanol/trypsin tolerance and transformation of notoginsenosides Authors: Cao, L.J. / Lin, M.Y. / Zhang, R. / Huang, Z.X. / Zhou, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i0x.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i0x.ent.gz | 177.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i0x_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 8i0x_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 8i0x_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 8i0x_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i0x ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i0x | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 58330.441 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas sp. (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A3G6ZHU4 #2: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16% PEG 3350,100 mM BIS-TRIS propane pH 8.5, 20.00 mM Sodium Potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→32.64 Å / Num. obs: 75588 / % possible obs: 97.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rpim(I) all: 0.1385 / Rrim(I) all: 0.3529 / Net I/σ(I): 6.37 |
Reflection shell | Resolution: 1.999→2.071 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 7109 / CC1/2: 0.515 / CC star: 0.825 / % possible all: 94.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→32.64 Å / SU ML: 0.1881 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.6381 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.64 Å
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Refine LS restraints |
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LS refinement shell |
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