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- PDB-4duv: E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4duv | ||||||
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Title | E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzyme and bis-Tris complex | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / bi-functional enzyme / allolactose synthesis / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH / BETA-GALACTOSIDASE / GLYCOSIDASE | ||||||
Function / homology | ![]() alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wheatley, R.W. / Lo, S. / Janzcewicz, L.J. / Dugdale, M.L. / Huber, R.E. | ||||||
![]() | ![]() Title: The Glucose Acceptor site of lacZ beta-galactosidase for the synthesis of allolactose - the natural inducer of the lac operon Authors: Wheatley, R.W. / Lo, S. / Janzcewicz, L.J. / Dugdale, M.L. / Huber, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 931.3 KB | Display | ![]() |
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PDB format | ![]() | 742.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 550.1 KB | Display | ![]() |
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Full document | ![]() | 574.4 KB | Display | |
Data in XML | ![]() | 173.8 KB | Display | |
Data in CIF | ![]() | 265.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jyxS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/2DG.gif)
![](data/chem/img/2DG.gif)
#1: Protein | Mass: 119757.773 Da / Num. of mol.: 4 / Fragment: unp residues 10-1024 / Mutation: G794A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-2DG / |
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-Non-polymers , 5 types, 4137 molecules ![](data/chem/img/BTB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BTB / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-DMS / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 8000, 100 MM BIS-TRIS, 200 MM MGCL2, 100 MM NACL, 10 MM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2007 |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (Si(111)) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11589 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→200 Å / Num. all: 295878 / Num. obs: 295878 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JYX Resolution: 2.1→86.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.994 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.156 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.263 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→86.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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