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Yorodumi- PDB-2rgl: Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rgl | ||||||
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Title | Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / beta-alpha-barrels / Glycosidase | ||||||
Function / homology | Function and homology information amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase ...amygdalin beta-glucosidase activity / prunasin beta-glucosidase activity / beta-L-arabinosidase activity / cellobiose glucosidase activity / beta-gentiobiose beta-glucosidase activity / beta-D-fucosidase activity / beta-mannosidase activity / glucan endo-1,3-beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process / protein homodimerization activity / extracellular region Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chuenchor, W. / Ketudat Cairns, J.R. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Chen, C.-J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Insights into Rice BGlu1 beta-Glucosidase Oligosaccharide Hydrolysis and Transglycosylation Authors: Chuenchor, W. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Oonanant, W. / Bevan, D.R. / Esen, A. / Chen, C.J. / Opassiri, R. / Svasti, J. / Cairns, J.R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rgl.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rgl.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 2rgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rgl ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rgl | HTTPS FTP |
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-Related structure data
Related structure data | 2rgmC 1cbgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 6 - 476 / Label seq-ID: 11 - 481
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54728.465 Da / Num. of mol.: 2 / Fragment: Residues UNP 29-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Species: Oryza sativa / Strain: Orion / Gene: Os3bglu7 / Plasmid: pET32a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) References: UniProt: Q42975, UniProt: Q75I93*PLUS, beta-glucosidase |
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-Non-polymers , 5 types, 1194 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 23% PEG MME 5000, 0.17M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.98008 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 53089 / Num. obs: 53040 / % possible obs: 99.91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5218 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBG Resolution: 2.2→29.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.597 / SU ML: 0.119 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.28 / ESU R Free: 0.192 / Stereochemistry target values: Engh & Huber
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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: 12.246 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3801 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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