+Open data
-Basic information
Entry | Database: PDB / ID: 7f3a | ||||||
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Title | Arabidopsis thaliana GH1 beta-glucosidase AtBGlu42 | ||||||
Components | Beta-glucosidase 42 | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 1 / beta-glucosidase | ||||||
Function / homology | Function and homology information induced systemic resistance, ethylene mediated signaling pathway / positive regulation of defense response / response to iron ion starvation / secondary metabolic process / scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / response to bacterium / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Horikoshi, S. / Saburi, W. / Yu, J. / Yao, M. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2022 Title: Substrate specificity of glycoside hydrolase family 1 beta-glucosidase AtBGlu42 from Arabidopsis thaliana and its molecular mechanism. Authors: Horikoshi, S. / Saburi, W. / Yu, J. / Matsuura, H. / Cairns, J.R.K. / Yao, M. / Mori, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f3a.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f3a.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 7f3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f3a_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 7f3a_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 7f3a_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 7f3a_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f3a ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f3a | HTTPS FTP |
-Related structure data
Related structure data | 3gnoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56230.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BGLU42, At5g36890, MLF18.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIW4, beta-glucosidase | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 9% (w/v) PEG 8000, 0.1 M calcium acetate, 0.05 M sodium cacodylate buffer (pH 6.5) |
-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: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→46.553 Å / Num. obs: 53471 / % possible obs: 99.97 % / Redundancy: 6.76 % / CC1/2: 0.999 / Rrim(I) all: 0.081 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.87 % / Mean I/σ(I) obs: 2 / Num. unique obs: 8612 / CC1/2: 0.783 / Rrim(I) all: 0.849 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3gno Resolution: 1.7→46.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.19 / Stereochemistry target values: ML
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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 max: 73.76 Å2 / Biso mean: 25.9446 Å2 / Biso min: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→46.553 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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