+Open data
-Basic information
Entry | Database: PDB / ID: 3scn | ||||||
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Title | Crystal Structure of Rice BGlu1 E386G Mutant | ||||||
Components | Beta-glucosidase 7 | ||||||
Keywords | HYDROLASE / BETA-ALPHA-BARRELS / GLYCOSYNTHASE / OLIGOSACCHARIDE SYNTHESIS / TRANSGLUCOSYLATION | ||||||
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 activity ...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 activity / beta-glucosidase / beta-galactosidase 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 | Pengthaisong, S. / Withers, S.G. / Kuaprasert, B. / Ketudat Cairns, J.R. | ||||||
Citation | Journal: to be published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3scn.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3scn.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 3scn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/3scn ftp://data.pdbj.org/pub/pdb/validation_reports/sc/3scn | HTTPS FTP |
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-Related structure data
Related structure data | 3scoC 3scpC 3scqC 3scrC 3scsC 3sctC 3scuC 3scvC 3scwC 2rglS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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
#1: Protein | Mass: 54656.402 Da / Num. of mol.: 2 / Mutation: E386G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Strain: ORION Gene: BGLU1, BGLU7, LOC_Os03g49600, Os03g0703000, os3bglu7, OSJNBa0004L11.16 Plasmid: pET32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q75I93, beta-glucosidase #2: Chemical | ChemComp-ZN / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THIS CONFLICT IS IN GENBANK DATABASE AAA84906. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 24% PEG MME 5000, 0.16M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 51498 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.114 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 4838 / Rsym value: 0.463 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RGL Resolution: 2.2→24.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.648 / SU ML: 0.146 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.224 / 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: 16.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→24.84 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: 3804 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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