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Yorodumi- PDB-4ucf: Crystal structure of Bifidobacterium bifidum beta-galactosidase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ucf | |||||||||
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Title | Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.94 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 Alpha-Galactose. Authors: Godoy, A.S. / Camilo, C.M. / Kadowaki, M.A. / Muniz, H.D. / 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 | 4ucf.cif.gz | 447.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ucf.ent.gz | 362.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ucf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4ucf ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4ucf | HTTPS FTP |
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-Related structure data
Related structure data | 4uzsSC 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
#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 #2: Sugar | ChemComp-GLA / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-POL / | #5: 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: NONE |
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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: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.8 Å / Num. obs: 153059 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UZS Resolution: 1.94→110.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.36 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDECHAINS WERE REMOVED FROM MODEL
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→110.51 Å
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Refine LS restraints |
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