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Yorodumi- PDB-4jaw: Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jaw | ||||||
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Title | Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline | ||||||
Components | Lacto-N-biosidase | ||||||
Keywords | HYDROLASE / alpha/beta-domain / Tim Barrel / beta-Trefoil / Membrane-anchored extracellular | ||||||
Function / homology | Function and homology information lacto-N-biosidase / lacto-N-biosidase activity / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / plasma membrane Similarity search - Function | ||||||
Biological species | Bifidobacterium bifidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Ito, T. / Katayama, T. / Stubbs, K.A. / Fushinobu, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum Authors: Ito, T. / Katayama, T. / Hattie, M. / Sakurama, H. / Wada, J. / Suzuki, R. / Ashida, H. / Wakagi, T. / Yamamoto, K. / Stubbs, K.A. / Fushinobu, S. #1: Journal: Appl.Environ.Microbiol. / Year: 2008 Title: Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure. Authors: Wada, J. / Ando, T. / Kiyohara, M. / Ashida, H. / Kitaoka, M. / Yamaguchi, M. / Kumagai, H. / Katayama, T. / Yamamoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jaw.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jaw.ent.gz | 209.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4jaw ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4jaw | HTTPS FTP |
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-Related structure data
Related structure data | 4h04SC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 71892.227 Da / Num. of mol.: 2 / Fragment: UNP Residue 41-663 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Strain: JCM1254 / Gene: lnbB / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: B3TLD6, lacto-N-biosidase #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-SO4 / #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: 2.79 Å3/Da / Density % sol: 55.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 25, 2012 |
Radiation | Monochromator: Si(111), numerical link type double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 150089 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.102 / Net I/σ(I): 23.97 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.85 / Num. unique all: 7436 / Rsym value: 0.485 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4H04 Resolution: 1.8→43.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.879 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 11.513 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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