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Yorodumi- PDB-3tts: Crystal structure of beta-galactosidase from Bacillus circulans s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tts | ||||||
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Title | Crystal structure of beta-galactosidase from Bacillus circulans sp. alkalophilus | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / Tim Barrel / Glycoside hydrolase | ||||||
Function / homology | Function and homology information Class I glutamine amidotransferase (GATase) domain / Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacillus circulans subsp. alkalophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Maksimainen, M. / Hakulinen, N. / Rouvinen, J. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Structural analysis, enzymatic characterization, and catalytic mechanisms of beta-galactosidase from Bacillus circulans sp. alkalophilus. Authors: Maksimainen, M. / Paavilainen, S. / Hakulinen, N. / Rouvinen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tts.cif.gz | 823.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tts.ent.gz | 681.8 KB | Display | PDB format |
PDBx/mmJSON format | 3tts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/3tts ftp://data.pdbj.org/pub/pdb/validation_reports/tt/3tts | HTTPS FTP |
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-Related structure data
Related structure data | 3ttyC 1kwgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 77413.359 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Bacillus circulans subsp. alkalophilus (bacteria) References: beta-galactosidase #2: Chemical | ChemComp-ZN / #3: 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: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 6-9% PEG 3350, 0.1M magnesium sulfate, 0.1M bicine, pH 8,5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 519617 / Num. obs: 182304 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 26.48 Å2 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KWG Resolution: 2.401→47.337 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 20.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.141 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.401→47.337 Å
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Refine LS restraints |
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LS refinement shell |
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