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Yorodumi- PDB-6ik8: Crystal structure of tomato beta-galactosidase (TBG) 4 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ik8 | |||||||||
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Title | Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,6-galactobiose | |||||||||
Components | Beta-galactosidase | |||||||||
Keywords | HYDROLASE / Glycoside Hydrolase / Plant cell wall related enzyme / Fruit ripening | |||||||||
Function / homology | Function and homology information beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Matsuyama, K. / Nakae, S. / Igarashi, K. / Tada, T. / Ishimaru, M. | |||||||||
Citation | Journal: Planta / Year: 2020 Title: Substrate-recognition mechanism of tomato beta-galactosidase 4 using X-ray crystallography and docking simulation. Authors: Matsuyama, K. / Kondo, T. / Igarashi, K. / Sakamoto, T. / Ishimaru, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ik8.cif.gz | 294.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ik8.ent.gz | 235.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ik8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/6ik8 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/6ik8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ik5C 6ik6C 6ik7C 3w5gS 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: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 22 - 726 / Label seq-ID: 5 - 709
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-Components
-Protein / Non-polymers , 2 types, 256 molecules BA
#1: Protein | Mass: 79726.914 Da / Num. of mol.: 2 / Mutation: E181A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Tissue: fruit / Gene: TBG4 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: O81100, beta-galactosidase #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 7 molecules
#2: Polysaccharide | #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | ChemComp-GAL / | |
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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: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 16% (w/v) PEG10000, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35773 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.413 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 3 / Num. unique obs: 1744 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5G Resolution: 2.8→48.02 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / SU B: 16.503 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / 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: 52.378 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→48.02 Å
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Refine LS restraints |
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