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Yorodumi- PDB-4uni: beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uni | ||||||||||||
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Title | beta-(1,6)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04 in complex with galactose | ||||||||||||
Components | BETA-GALACTOSIDASE | ||||||||||||
Keywords | HYDROLASE / GH42 | ||||||||||||
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 | BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Viborg, A.H. / Fredslund, F. / Katayama, T. / Nielsen, S.K. / Svensson, B. / Kitaoka, M. / Lo Leggio, L. / Abou Hachem, M. | ||||||||||||
Citation | Journal: Mol. Microbiol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uni.cif.gz | 746.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uni.ent.gz | 630.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uni_validation.pdf.gz | 506.4 KB | Display | wwPDB validaton report |
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Full document | 4uni_full_validation.pdf.gz | 541 KB | Display | |
Data in XML | 4uni_validation.xml.gz | 76 KB | Display | |
Data in CIF | 4uni_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/4uni ftp://data.pdbj.org/pub/pdb/validation_reports/un/4uni | HTTPS FTP |
-Related structure data
Related structure data | 4uoqC 4uozC 1kwgS 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 78328.281 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS (bacteria) Strain: BL-04 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: C6A6W5, beta-galactosidase #2: Sugar | |
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-Non-polymers , 5 types, 361 molecules
#3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-ZN / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: 27% PEG1500, 0.01 M MGCL2, 0.1 M MMT BUFFER PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04094 |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Sep 28, 2011 / 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: 1.04094 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 92722 / % possible obs: 99.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.07 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KWG Resolution: 2.6→29.727 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 25.96 / 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: 2.6→29.727 Å
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Refine LS restraints |
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LS refinement shell |
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