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- PDB-3scq: Crystal Structure of Rice BGlu1 E386A Mutant Complexed with alpha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3scq | ||||||
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Title | Crystal Structure of Rice BGlu1 E386A Mutant Complexed with alpha-Glucosyl Fluoride | ||||||
![]() | Beta-glucosidase 7 | ||||||
![]() | HYDROLASE / BETA-ALPHA-BARRELS / GLYCOSYNTHASE / OLIGOSACCHARIDE SYNTHESIS / TRANSGLUCOSYLATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Pengthaisong, S. / Withers, S.G. / Kuaprasert, B. / Ketudat Cairns, J.R. | ||||||
![]() | ![]() Title: Structural investigation of the basis for cellooligosaccharide synthesis by rice BGlu1 glycosynthases Authors: Pengthaisong, S. / Withers, S.G. / Kuaprasert, B. / 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 | ![]() | 218 KB | Display | ![]() |
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PDB format | ![]() | 169.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.4 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 62.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3scnC ![]() 3scoC ![]() 3scpC ![]() 3scrC ![]() 3scsC ![]() 3sctC ![]() 3scuC ![]() 3scvC ![]() 3scwC ![]() 2rglS 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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2 | ![]()
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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![](data/chem/img/GLF.gif)
![](data/chem/img/GLF.gif)
#1: Protein | Mass: 54670.430 Da / Num. of mol.: 2 / Mutation: E386A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ORION Gene: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, os3bglu7, OSJNBa0004L11.16 Plasmid: pET32a(+) / Production host: ![]() ![]() #5: Sugar | |
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-Non-polymers , 4 types, 787 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)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THIS CONFLICT IS IN GENBANK DATABASE AAA84906. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 22% PEG MME 5000, 0.16M ammonium sulfate, 0.1M MES, 0.010M alpha-glucosyl fluoride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 60561 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.123 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 5870 / Rsym value: 0.439 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RGL Resolution: 2.1→25.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.946 / SU ML: 0.106 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.168 / 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: 11.764 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25.01 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: 3805 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.095→2.149 Å / Total num. of bins used: 20
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