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- PDB-6ik7: Crystal structure of tomato beta-galactosidase (TBG) 4 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ik7 | |||||||||
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Title | Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose | |||||||||
![]() | Beta-galactosidase | |||||||||
![]() | HYDROLASE / Glycoside hydrolase / plant / plant cell wall related enzyme / Fruit ripening | |||||||||
Function / homology | ![]() beta-galactosidase / beta-galactosidase activity / vacuole / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Matsuyama, K. / Nakae, S. / Igarashi, K. / Tada, T. / Ishimaru, M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.5 KB | Display | ![]() |
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PDB format | ![]() | 230.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ik5C ![]() 6ik6C ![]() 6ik8C ![]() 3w5gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 79726.914 Da / Num. of mol.: 2 / Mutation: E181A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 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: 3.1→50 Å / Num. obs: 27531 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.083 / Rrim(I) all: 0.223 / Net I/σ(I): 10.624 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.8 / Num. unique obs: 1354 / Rpim(I) all: 0.319 / Rrim(I) all: 0.863 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W5G Resolution: 3.1→43.43 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.31 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→43.43 Å
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Refine LS restraints |
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