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- PDB-4uoq: Nucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uoq | ||||||
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Title | Nucleophile mutant (E324A) of beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 | ||||||
![]() | BETA-GALACTOSIDASE![]() | ||||||
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Function / homology | ![]() Class I glutamine amidotransferase (GATase) domain / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Viborg, A.H. / Fredslund, F. / Katayama, T. / Nielsen, S.K. / Svensson, B. / Kitaoka, M. / Lo Leggio, L. / Abou Hachem, M. | ||||||
![]() | ![]() Title: A beta 1-6/ beta 1-3 galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 gives insight into sub-specificities of beta-galactoside catabolism within Bifidobacterium. Authors: Viborg, A.H. / Fredslund, F. / Katayama, T. / Nielsen, S.K. / Svensson, B. / Kitaoka, M. / Lo Leggio, L. / Abou Hachem, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.8 KB | Display | ![]() |
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PDB format | ![]() | 337.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uniSC ![]() 4uozC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | ![]() Mass: 78270.242 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BL-04 / Plasmid: PET28A / Production host: ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 316 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-PGE / ![]() #4: Chemical | ChemComp-PEG / ![]() #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 62.36 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: 29% PEG1500, 0.01 MM MGCL2, 0.1 M MMT BUFFER PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Sep 10, 2012 / Details: MIRRORS |
Radiation | Monochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→20 Å / Num. obs: 85508 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 46.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.65 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4UNI Resolution: 2.7→19.93 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 24.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.93 Å
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Refine LS restraints |
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LS refinement shell |
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