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Yorodumi- PDB-3scu: Crystal Structure of Rice BGlu1 E386G Mutant Complexed with Cello... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3scu | |||||||||
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Title | Crystal Structure of Rice BGlu1 E386G Mutant Complexed with Cellopentaose | |||||||||
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 ...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: 1.58 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 | 3scu.cif.gz | 224.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3scu.ent.gz | 175.3 KB | Display | PDB format |
PDBx/mmJSON format | 3scu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/3scu ftp://data.pdbj.org/pub/pdb/validation_reports/sc/3scu | HTTPS FTP |
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-Related structure data
Related structure data | 3scnC 3scoC 3scpC 3scqC 3scrC 3scsC 3sctC 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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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
#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: Polysaccharide | |
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-Non-polymers , 4 types, 927 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
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: 47.21 % |
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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, 0.002M cellopentaose, 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: Jan 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→30 Å / Num. obs: 139830 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.071 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 13832 / Rsym value: 0.455 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RGL Resolution: 1.58→28.02 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.304 / SU ML: 0.047 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.079 / 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: 13.144 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→28.02 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: 1.58→1.621 Å / Total num. of bins used: 20
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