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- PDB-3f5l: Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f5l | |||||||||
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Title | Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta-glucosidase | |||||||||
![]() | Beta-glucosidase | |||||||||
![]() | HYDROLASE / beta-alpha-barrels / Glycosidase | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chuenchor, W. / Ketudat Cairns, J.R. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Chen, C.-J. | |||||||||
![]() | ![]() Title: The structural basis of oligosaccharide binding by rice BGlu1 beta-glucosidase Authors: Chuenchor, W. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Svasti, J. / Ketudat Cairns, J.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.8 KB | Display | ![]() |
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PDB format | ![]() | 181.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 47.5 KB | Display | |
Data in CIF | ![]() | 74.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ahtC ![]() 3ahvC ![]() 3f4vC ![]() 3f5jC ![]() 3f5kC ![]() 1cbgS 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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1 | ![]()
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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: ASN / Beg label comp-ID: ASN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 5 - 476 / Label seq-ID: 10 - 481
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 54727.480 Da / Num. of mol.: 2 / Fragment: UNP Residues 29-504 / Mutation: E176Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Orion / Gene: Os3bglu7 / Plasmid: pET32a+ / Production host: ![]() ![]() References: UniProt: Q42975, UniProt: Q75I93*PLUS, beta-glucosidase #2: Polysaccharide | |
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-Non-polymers , 4 types, 1307 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.43 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 22% PEG MME 5000, 0.18M 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 218817 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.22 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.95 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CBG Resolution: 1.37→28.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.851 / SU ML: 0.034 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.059 / 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: 12.445 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→28.06 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: 3809 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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