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Yorodumi- PDB-3aiv: Crystal structure of beta-glucosidase in rye complexed with an ag... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aiv | ||||||
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Title | Crystal structure of beta-glucosidase in rye complexed with an aglycone DIMBOA | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / TIM barrel | ||||||
Function / homology | Function and homology information 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase / DIMBOA glucoside beta-D-glucosidase activity / scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / chloroplast / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Secale cereale (rye) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sue, M. / Nakamura, C. / Miyamoto, T. / Yajima, S. | ||||||
Citation | Journal: Plant Sci. / Year: 2011 Title: Active-site architecture of benzoxazinone-glucoside beta-D-glucosidases in Triticeae Authors: Sue, M. / Nakamura, C. / Miyamoto, T. / Yajima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aiv.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aiv.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 3aiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3aiv ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3aiv | HTTPS FTP |
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-Related structure data
Related structure data | 3aiqC 3airC 3aisC 3aiuC 3aiwC 2dgaS 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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-Components
#1: Protein | Mass: 63971.230 Da / Num. of mol.: 1 / Fragment: residues in UNP 50-568 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Secale cereale (rye) / Gene: ScGlu / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus(de3) Ril / References: UniProt: Q9FYS3, beta-glucosidase |
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#2: Chemical | ChemComp-HBO / |
#3: Water | ChemComp-HOH / |
Sequence details | THE DEPOSITORS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 20mM HEPES, 1M LiSO4, 150mM NaCl, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2006 |
Radiation | Monochromator: triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 43816 / % possible obs: 99.9 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 16.1 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DGA Resolution: 2.5→47.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.036 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.169 / 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: 24.632 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.564 Å / Total num. of bins used: 20
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