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Open data
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Basic information
Entry | Database: PDB / ID: 1jyw | |||||||||
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Title | E. COLI (lacZ) BETA-GALACTOSIDASE (E537Q) IN COMPLEX WITH PNPG | |||||||||
![]() | Beta-Galactosidase | |||||||||
![]() | HYDROLASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Juers, D.H. / Matthews, B.W. | |||||||||
![]() | ![]() Title: A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Authors: Juers, D.H. / Heightman, T.D. / Vasella, A. / McCarter, J.D. / Mackenzie, L. / Withers, S.G. / Matthews, B.W. #1: ![]() Title: High Resolution Structure of Beta-Galactosidase in a New Crystal Form Reveals Multiple Metal-Binding Sites and Provides a Structural Basis for Alpha-Complementation Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W. #2: ![]() Title: Structural Comparisons of Tim Barrel Proteins Suggest Functional and Evolutionary Relationships between Beta-Galactosidase and Other Glycohydrolases Authors: Juers, D.H. / Huber, R.E. / Matthews, B.W. #3: ![]() Title: Three-Dimensional Structure of Beta-Galactosidase from E. Coli Authors: Jacobson, R.H. / Zhang, X.J. / Dubose, R.F. / Matthews, B.W. #4: ![]() Title: Crystallization of beta-galactosidase from Escherichia coli Authors: Jacobson, R.H. / Matthews, B.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 948 KB | Display | ![]() |
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PDB format | ![]() | 746.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 197 KB | Display | |
Data in CIF | ![]() | 298.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jynC ![]() 1jyvC ![]() 1jyxC ![]() 1jz2C ![]() 1jz3C ![]() 1jz4C ![]() 1jz5C ![]() 1jz6C ![]() 1jz7C ![]() 1jz8C ![]() 4v44C ![]() 4v45C ![]() 1dp0S 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 8 molecules ABCD![](data/chem/img/147.gif)
![](data/chem/img/147.gif)
#1: Protein | Mass: 116505.281 Da / Num. of mol.: 4 / Mutation: E537Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-147 / |
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-Non-polymers , 4 types, 4602 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: 2.7 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Bis-Tris, PEG 8000, MgCl2, NaCl, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 288K, pH 6.50 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: used macroseeding, Juers, D.H., (2000) Protein Sci., 9, 1685. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8984 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28.8 Å / Num. all: 715525 / Num. obs: 715525 / % possible obs: 98.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10 |
Reflection shell | Highest resolution: 1.55 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 95.8 |
Reflection | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DP0 Resolution: 1.55→28.8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: TNT
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Solvent computation | Solvent model: BABINET PRINCIPLE / Bsol: 225 Å2 / ksol: 0.83 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→28.8 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection Rfree: 10563 / % reflection Rfree: 1.5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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