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Yorodumi- PDB-4jie: Structural analysis and insights into glycon specificity of the r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jie | ||||||
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Title | Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase | ||||||
Components | Beta-mannosidase/beta-glucosidase | ||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE FAMILY 1 / BETA-D-MANNOSIDASE / ORYZA SATIVA / TIM BARREL / GLYCOSIDE HYDROLASE | ||||||
Function / homology | Function and homology information beta-mannosidase / beta-D-fucosidase activity / beta-mannosidase activity / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Oryza sativa Indica Group (long-grained rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 2.45 Å | ||||||
Authors | Tankrathok, A. / Luang, S. / Robinson, R.C. / Kimura, A. / Hrmova, M. / Ketudat Cairns, J.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase Authors: Tankrathok, A. / Iglesias-Fernandez, J. / Luang, S. / Robinson, R.C. / Kimura, A. / Rovira, C. / Hrmova, M. / 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 | 4jie.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jie.ent.gz | 88.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/4jie ftp://data.pdbj.org/pub/pdb/validation_reports/ji/4jie | HTTPS FTP |
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-Related structure data
Related structure data | 4jhoC 2rglS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57775.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice) Production host: Escherichia coli (E. coli) References: UniProt: B5ABY0, UniProt: A2YPH1*PLUS, beta-mannosidase | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-EPE / | #4: Sugar | ChemComp-BMA / | #5: 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: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: 0.8M K/Na tartrate, 0.1M Na HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.25→27.82 Å / Num. obs: 29353 / % possible obs: 77.53 % / Observed criterion σ(I): 1 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Refinement Starting model: 2RGL Resolution: 2.45→26.22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.981 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.232 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→26.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.453→2.516 Å / Total num. of bins used: 20
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