+Open data
-Basic information
Entry | Database: PDB / ID: 1jyx | ||||||
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Title | E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH IPTG | ||||||
Components | Beta-Galactosidase | ||||||
Keywords | HYDROLASE / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / IMMUNOGLOBULIN / BETA SUPERSANDWICH | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Juers, D.H. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2001 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: Journal: Protein Sci. / Year: 2000 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: Journal: Protein Sci. / Year: 1999 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: Journal: Nature / Year: 1994 Title: Three-Dimensional Structure of Beta-Galactosidase from E. Coli Authors: Jacobson, R.H. / Zhang, X.J. / Dubose, R.F. / Matthews, B.W. #4: Journal: J.Mol.Biol. / Year: 1992 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jyx.cif.gz | 918.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jyx.ent.gz | 727.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jyx ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jyx | HTTPS FTP |
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-Related structure data
Related structure data | 1jynC 1jyvC 1jywC 1jz2C 1jz3C 1jz4C 1jz5C 1jz6C 1jz7C 1jz8C 4v44C 4v45C 1dp0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 10 molecules ABCD
#1: Protein | Mass: 116506.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00722, beta-galactosidase #4: Sugar | ChemComp-IPT / |
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-Non-polymers , 4 types, 3704 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / #5: Chemical | ChemComp-DMS / #6: 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: 2.7 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 pH: 6.5 / 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 1998 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→17 Å / Num. all: 444288 / Num. obs: 444288 / % possible obs: 89.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 | |||||||||
Reflection shell | Highest resolution: 1.75 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 88 | |||||||||
Reflection | *PLUS % possible obs: 90 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 | |||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DP0 Resolution: 1.75→27 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT
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Solvent computation | Solvent model: BABINET PRINCIPLE / Bsol: 127 Å2 / ksol: 0.74 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→27 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 1.5 % / Rfactor obs: 0.168 / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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