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Yorodumi- PDB-3w5g: Crystal structure of tomato beta-galactosidase 4 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w5g | |||||||||
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Title | Crystal structure of tomato beta-galactosidase 4 in complex with galactose | |||||||||
Components | Beta-galactosidase | |||||||||
Keywords | HYDROLASE / Tim Barrel / beta-Sandwich / Glycosylation | |||||||||
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: 3 Å | |||||||||
Authors | Eda, M. / Tada, T. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of tomato beta-galactosidase 4 in complex with galactose Authors: Eda, M. / Tada, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5g.cif.gz | 286.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5g.ent.gz | 230 KB | Display | PDB format |
PDBx/mmJSON format | 3w5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5g ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5g | HTTPS FTP |
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-Related structure data
Related structure data | 3w5fS 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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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.) Solanum lycopersicum (tomato) / Gene: TBG4 / Plasmid: pPICZ alpha A / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: O81100, beta-galactosidase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | #4: Sugar | ChemComp-GAL / #5: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 20% (w/v) PEG 10000, 0.1M D-galactose, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 33114 / Num. obs: 32837 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5F Resolution: 3→31.06 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / 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: 47.29 Å2
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Refinement step | Cycle: LAST / Resolution: 3→31.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.004→3.082 Å / Total num. of bins used: 20
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