+Open data
-Basic information
Entry | Database: PDB / ID: 5bxr | ||||||
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Title | LNBase in complex with LNB-NHAcDNJ | ||||||
Components | Lacto-N-biosidase | ||||||
Keywords | HYDROLASE / TIM barrel / distal gut / Human milk oligosaccharides / Inhibitor | ||||||
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 JCM 1254 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Ito, T. / Arakawa, T. / Fushinobu, S. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2015 Title: Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis Authors: Hattie, M. / Ito, T. / Debowski, A.W. / Arakawa, T. / Katayama, T. / Yamamoto, K. / Fushinobu, S. / Stubbs, K.A. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bxr.cif.gz | 277.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bxr.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 5bxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/5bxr ftp://data.pdbj.org/pub/pdb/validation_reports/bx/5bxr | HTTPS FTP |
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-Related structure data
Related structure data | 5bxpC 5bxsC 5bxtC 4h04S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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 residues 41-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria) Gene: lnbB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M potassium sodium tartate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 189858 / % possible obs: 90 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.92 / % possible all: 95.2 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4H04 Resolution: 1.6→28.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.605 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 17.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.19 Å
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Refine LS restraints |
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