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- PDB-3gnp: Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gnp | ||||||
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Title | Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-Beta-D-Thio-Glucoside | ||||||
![]() | Os03g0212800 protein | ||||||
![]() | HYDROLASE / BETA-ALPHA BARREL / GLYCOSIDASE | ||||||
Function / homology | ![]() cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / hydrolase activity, acting on glycosyl bonds / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seshadri, S. / Akiyama, T. / Opassiri, R. / Kuaprasert, B. / Cairns, J.R.K. | ||||||
![]() | ![]() Title: Structural and enzymatic characterization of Os3BGlu6, a rice {beta}-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides. Authors: Seshadri, S. / Akiyama, T. / Opassiri, R. / Kuaprasert, B. / Cairns, J.R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.2 KB | Display | ![]() |
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PDB format | ![]() | 88.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781 KB | Display | ![]() |
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Full document | ![]() | 786.6 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gnoSC ![]() 3gnrC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 55316.934 Da / Num. of mol.: 1 / Fragment: UNP residues 38-521 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 Plasmid: pET32A+/DEST / Production host: ![]() ![]() | ||
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#2: Sugar | ChemComp-SOG / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 19% PEG5000 MME, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 49796 / Num. obs: 48102 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 6.4 / Num. unique all: 5274 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GNO Resolution: 1.8→26.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.803 / SU ML: 0.085 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.117 / 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: 19.485 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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