+Open data
-Basic information
Entry | Database: PDB / ID: 4uzs | ||||||
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Title | Crystal structure of Bifidobacterium bifidum beta-galactosidase | ||||||
Components | BETA-GALACTOSIDASE | ||||||
Keywords | HYDROLASE / LACTASE / FAMILY 42 | ||||||
Function / homology | Function and homology information galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity Similarity search - Function | ||||||
Biological species | BIFIDOBACTERIUM BIFIDUM S17 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.74 Å | ||||||
Authors | Godoy, A.S. / Murakami, M.T. / Camilo, C.M. / Bernardes, A. / Polikarpov, I. | ||||||
Citation | Journal: FEBS J. / Year: 2016 Title: Crystal Structure of Beta1-6-Galactosidase from Bifidobacterium Bifidum S17: Trimeric Architecture, Molecular Determinants of the Enzymatic Activity and its Inhibition by Alpah-Galactose. Authors: Godoy, A.S. / Camilo, C.M. / Kadowaki, M.A. / Muniz, H.D.S. / Santo, M.E. / Murakami, M.T. / Nascimento, A.S. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uzs.cif.gz | 466 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uzs.ent.gz | 381.7 KB | Display | PDB format |
PDBx/mmJSON format | 4uzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uzs ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uzs | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 77278.234 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BIFIDOBACTERIUM BIFIDUM S17 (bacteria) Description: COURTESY OF PROF. CHRISTIAN RIEDEL, ULM UNIVERSITY, GERMANY Plasmid: PPROEX HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E3EPA1, beta-galactosidase |
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-Non-polymers , 5 types, 2713 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-P6G / | #5: Chemical | ChemComp-POL / #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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: CRYSTALS DERIVATED WITH HG |
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Crystal grow | Temperature: 292 K / pH: 6 Details: 20% (W/V) POLYETHYLENE GLYCOL 3, 350, 0.2 M DIBASIC AMMONIUM TARTRATE AND 4% (W/V) 1-PROPANOL AT 292 K, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2010 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.7 Å / Num. obs: 200160 / % possible obs: 98.5 % / Observed criterion σ(I): 1.8 / Redundancy: 3.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.74→35.772 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→35.772 Å
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Refine LS restraints |
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LS refinement shell |
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