[English] 日本語
Yorodumi- PDB-3ues: Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ues | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis complexed with deoxyfuconojirimycin | ||||||
Components | Alpha-1,3/4-fucosidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Tim Barrel / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | Bifidobacterium longum subsp. infantis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sakurama, H. / Fushinobu, S. / Yoshida, E. / Honda, Y. / Hidaka, M. / Ashida, H. / Kitaoka, M. / Katayama, T. / Yamamoto, K. / Kumagai, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: 1,3-1,4-alpha-L-fucosynthase that specifically introduces Lewis a/x antigens into type-1/2 chains Authors: Sakurama, H. / Fushinobu, S. / Hidaka, M. / Yoshida, E. / Honda, Y. / Ashida, H. / Kitaoka, M. / Kumagai, H. / Yamamoto, K. / Katayama, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ues.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ues.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ues.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ues_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ues_full_validation.pdf.gz | 489.8 KB | Display | |
Data in XML | 3ues_validation.xml.gz | 47 KB | Display | |
Data in CIF | 3ues_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3ues ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3ues | HTTPS FTP |
-Related structure data
Related structure data | 3uetC 3mo4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53092.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria) Strain: ATCC15697 / Gene: BLIJ_2413, Blon_2336 / Plasmid: pET-30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(delta)lacZ (DE3) / References: UniProt: B7GNN8, EC: 3.2.1.111 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1M citrate buffer (pH 4.0), 20% (w/v) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2010 |
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: 1.6→50 Å / Num. all: 146360 / Num. obs: 146170 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 19 Å2 / Rsym value: 0.059 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 14451 / Rsym value: 0.335 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MO4 Resolution: 1.6→25.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.259 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.406 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.596→1.638 Å / Total num. of bins used: 20
|