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Yorodumi- PDB-3t0d: E.coli (lacZ) beta-galactosidase (S796T) in complex with galacton... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t0d | ||||||
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Title | E.coli (lacZ) beta-galactosidase (S796T) in complex with galactonolactone | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / Dynampic Loop Conformation / Ser-796 / TIM BARREL (ALPHA/BETA BARREL) / JELLY-ROLL BARREL / BETA SUPERSANDWICH / GLYCOSIDASE | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.93 Å | ||||||
Authors | Jancewicz, L.J. / Wheatley, R.W. / Sutendra, G. / Lee, M. / Fraser, M. / Huber, R.E. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2012 Title: Ser-796 of Beta-galactosidase (E. coli) plays a Key role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Authors: Jancewicz, L.J. / Wheatley, R.W. / Sutendra, G. / Lee, M. / Fraser, M.E. / Huber, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t0d.cif.gz | 927.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t0d.ent.gz | 739.6 KB | Display | PDB format |
PDBx/mmJSON format | 3t0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/3t0d ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t0d | HTTPS FTP |
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-Related structure data
Related structure data | 3sepC 3t08C 3t09C 3t0aC 3t0bC 3t2oC 3t2pC 3t2qC 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: 119757.773 Da / Num. of mol.: 4 / Fragment: Unp residues 10-1024 / Mutation: S796T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0344, JW0335, lacZ / Plasmid: pBAD/HIS/LacZ / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P00722, beta-galactosidase #2: Sugar | ChemComp-149 / |
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-Non-polymers , 4 types, 4148 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8-10% PEG 8000, 100 mM Bis-tris, 200 mM MgCl2, 100 mM NaCl, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2006 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: Double flat Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→162.2 Å / Num. all: 362650 / Num. obs: 362650 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.93→1.97 Å / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.93→75.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.956 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / 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: 23.467 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→75.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.983 Å / Total num. of bins used: 20
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