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- PDB-4dux: E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dux | ||||||
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Title | E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose | ||||||
![]() | 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: Structural explanation for allolactose (lac operon inducer) synthesis by lacZ beta-galactosidase and the evolutionary relationship between allolactose synthesis and the lac repressor. Authors: Wheatley, R.W. / Lo, S. / Jancewicz, 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 | ![]() | 883 KB | Display | ![]() |
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PDB format | ![]() | 711 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4duwC ![]() 1jyxS C: citing same article ( 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, 13 molecules ABCD![](data/chem/img/0MK.gif)
![](data/chem/img/0MK.gif)
#1: Protein | Mass: 119716.727 Da / Num. of mol.: 4 / Fragment: unp residues 10-1024 / Mutation: N460S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-0MK / |
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-Non-polymers , 4 types, 2716 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-DMS / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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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: 2.3→169.03 Å / Num. all: 224130 / Num. obs: 224130 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.6 / Num. unique all: 31819 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JYX Resolution: 2.3→86.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.011 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.205 / 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: 37.145 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→86.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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