+Open data
-Basic information
Entry | Database: PDB / ID: 8i0j | ||||||
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Title | JB13GH39P28 mutant-D41G | ||||||
Components | Glycoside hydrolase family 39 beta-xylosidase | ||||||
Keywords | HYDROLASE / beta-Xylosidase / salt/ethanol/trypsin tolerance / 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: 1.44 Å | ||||||
Authors | Zhou, J.P. / Cao, L.J. / Lin, M.Y. / Zhang, R. / Huang, Z.X. | ||||||
Funding support | China, 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 | 8i0j.cif.gz | 435.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i0j.ent.gz | 354 KB | Display | PDB format |
PDBx/mmJSON format | 8i0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i0j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8i0j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8i0j_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 8i0j_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i0j ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i0j | 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: 58272.395 Da / Num. of mol.: 2 / Mutation: D41G 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: Chemical | #3: Water | ChemComp-HOH / | 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: 2.21 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PACT G10 20% w/v PEG3350;100mM BIS-TRIS propane PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 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: 1.44→48 Å / Num. obs: 178820 / % possible obs: 98.86 % / Redundancy: 6.2 % / Biso Wilson estimate: 17.56 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.1189 / Rpim(I) all: 0.05393 / Rrim(I) all: 0.1314 / Net I/σ(I): 16.26 |
Reflection shell | Resolution: 1.44→1.491 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6319 / Mean I/σ(I) obs: 4.93 / Num. unique obs: 17942 / CC1/2: 0.926 / CC star: 0.981 / Rpim(I) all: 0.2574 / Rrim(I) all: 0.6832 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→48 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.889 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.061 / 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: 20.189 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→48 Å
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Refine LS restraints |
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