+
Open data
-
Basic information
Entry | Database: PDB / ID: 5bxp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | LNBase in complex with LNB-LOGNAc | |||||||||
![]() | Lacto-N-biosidase | |||||||||
![]() | HYDROLASE / TIM barrel / distal gut / Human milk oligosaccharides / Inhibitor | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ito, T. / Arakawa, T. / Fushinobu, S. | |||||||||
![]() | ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 278.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 222.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 55.8 KB | Display | |
Data in CIF | ![]() | 83.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bxrC ![]() 5bxsC ![]() 5bxtC ![]() 4h04S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 71892.227 Da / Num. of mol.: 2 / Fragment: UNP residues 41-663 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lnbB / Plasmid: pET28b / Production host: ![]() ![]() #2: Polysaccharide | Type: oligosaccharide / Mass: 396.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 175974 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.48 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4H04 Resolution: 1.7→29.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.834 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|