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Yorodumi- PDB-3f5k: Semi-active E176Q mutant of rice BGlu1, a plant exoglucanase/beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f5k | |||||||||
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Title | Semi-active E176Q mutant of rice BGlu1, 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: 1.8 Å | |||||||||
Authors | Chuenchor, W. / Ketudat Cairns, J.R. / Pengthaisong, S. / Robinson, R.C. / Yuvaniyama, J. / Chen, C.-J. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f5k.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f5k.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 3f5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/3f5k ftp://data.pdbj.org/pub/pdb/validation_reports/f5/3f5k | HTTPS FTP |
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-Related structure data
Related structure data | 3ahtC 3ahvC 3f4vC 3f5jC 3f5lC 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: 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.) Oryza sativa Japonica Group (Japanese rice) 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: Polysaccharide | |
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-Non-polymers , 5 types, 808 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: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 23% PEG MME 5000, 0.22M 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: BL13C1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 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: 1.8→30 Å / Num. all: 94774 / Num. obs: 93670 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.96 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.11 / Num. unique all: 16141 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBG Resolution: 1.8→27.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.501 / SU ML: 0.078 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.217 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.94 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: 1.802→1.849 Å / Total num. of bins used: 20
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