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- PDB-3wbe: Rice Os3BGlu6 Beta-Glucosidase E178Q mutant in a covalent complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wbe | ||||||
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Title | Rice Os3BGlu6 Beta-Glucosidase E178Q mutant in a covalent complex with Glc from GA4GE. | ||||||
![]() | Beta-glucosidase 6![]() | ||||||
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Function / homology | ![]() cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sansenya, S. / Hua, Y. / Cairns, J.R.K. | ||||||
![]() | ![]() Title: Enzymatic and structural characterization of hydrolysis of gibberellin A4 glucosyl ester by a rice beta-d-glucosidase Authors: Hua, Y. / Sansenya, S. / Saetang, C. / Wakuta, S. / 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 | ![]() | 124.6 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wbaC ![]() 3gnoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 55373.000 Da / Num. of mol.: 1 / Fragment: Os3BGlu6 beta-glucosidase, UNP residues 38-521 / Mutation: E178Q Source method: isolated from a genetically manipulated source Details: Originally cloned into pENTR/TEV/D-TOPO and subcloned into pET32a(+)/DEST. Source: (gene. exp.) ![]() ![]() ![]() Strain: Yukihikari / Gene: BGLU6, LOC_Os03g11420, Os03g0212800 / Plasmid: pET32a(+)/DEST / Production host: ![]() ![]() ![]() ![]() | ||||
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#2: Sugar | ChemComp-GLC / ![]() | ||||
#3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() Nonpolymer details | GLC(501) AND GOL(502) ARE IN ALTERNATE CONFORMATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13% PEG5000MME, 0.1M Bis/Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2011 / Details: toroidal mirror |
Radiation | Monochromator: LN2-cooled, fixed-exit double crystal monochromator, Si 111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→30 Å / Num. all: 41777 / Num. obs: 41752 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 6.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() Starting model: PDB ENTRY 3GNO Resolution: 1.97→23.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.392 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.122 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.554 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→23.52 Å
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Refine LS restraints |
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