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Yorodumi- PDB-2rgm: Rice BGlu1 beta-glucosidase, a plant exoglucanase/beta-glucosidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rgm | ||||||
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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: 1.55 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 | 2rgm.cif.gz | 233.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rgm.ent.gz | 181.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rgm ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rgm | HTTPS FTP |
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-Related structure data
Related structure data | 2rglC 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: 6 / Auth seq-ID: 6 - 476 / Label seq-ID: 11 - 481
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-Components
-Protein / Sugars , 2 types, 4 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 #2: Sugar | |
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-Non-polymers , 5 types, 1359 molecules
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 23% PEG MME 5000, 0.2M 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: 1.52→30 Å / Num. all: 157799 / Num. obs: 155944 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.29 / Num. unique all: 15186 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBG Resolution: 1.55→28.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.302 / SU ML: 0.048 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE WATERS LISTED IN REMARK 500 WERE CLEARLY EVIDENT IN THE DENSITY AND REFINED TO THESE POSITIONS, TYR 131 SEEMS TO HYDROGEN BOND WITH THE SAME OXYGEN (GLYCEROL O2) AS GLU176, WHICH IS THE ...Details: THE WATERS LISTED IN REMARK 500 WERE CLEARLY EVIDENT IN THE DENSITY AND REFINED TO THESE POSITIONS, TYR 131 SEEMS TO HYDROGEN BOND WITH THE SAME OXYGEN (GLYCEROL O2) AS GLU176, WHICH IS THE CATALYTIC ACID/BASE. GLU 386 IS COVALENTLY BOUND TO 2-FLUOROGLUCOSIDE AND THE SURROUNDING RESIDUES.
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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: 13.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→28.21 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: 3812 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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