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- PDB-6ik5: 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: 6ik5 | |||||||||
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Title | Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with galactose | |||||||||
![]() | Beta-galactosidase | |||||||||
![]() | HYDROLASE / Glycoside hydrolase / 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 | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 245.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 60.4 KB | Display | |
Data in CIF | ![]() | 88.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ik6C ![]() 6ik7C ![]() 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: 79784.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.55 % |
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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: Sep 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→41.28 Å / Num. obs: 123244 / % possible obs: 98.34 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.82→1.885 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 11826 / Rpim(I) all: 0.297 / Rrim(I) all: 0.782 / % possible all: 95.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W5G Resolution: 1.82→41.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.124 / 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: 24.951 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→41.28 Å
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Refine LS restraints |
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