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Yorodumi- PDB-1jz3: E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jz3 | ||||||
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Title | E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE | ||||||
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 | 1jz3.cif.gz | 938.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jz3.ent.gz | 745.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jz3_validation.pdf.gz | 570.6 KB | Display | wwPDB validaton report |
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Full document | 1jz3_full_validation.pdf.gz | 704.7 KB | Display | |
Data in XML | 1jz3_validation.xml.gz | 194 KB | Display | |
Data in CIF | 1jz3_validation.cif.gz | 294 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/1jz3 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/1jz3 | HTTPS FTP |
-Related structure data
Related structure data | 1jynC 1jyvC 1jywC 1jyxC 1jz2C 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, 8 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 #2: Sugar | ChemComp-2DG / |
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-Non-polymers , 5 types, 4441 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-BTB / #6: Chemical | ChemComp-DMS / #7: 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 13, 1998 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→16 Å / Num. all: 470782 / Num. obs: 470782 / % possible obs: 93.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14 | |||||||||
Reflection shell | Highest resolution: 1.75 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 87.5 | |||||||||
Reflection | *PLUS % possible obs: 94 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.061 | |||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DP0 Resolution: 1.75→16 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: TNT
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Solvent computation | Solvent model: BABINET PRINCIPLE / Bsol: 115 Å2 / ksol: 0.7 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→16 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.158 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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