+Open data
-Basic information
Entry | Database: PDB / ID: 6a86 | ||||||
---|---|---|---|---|---|---|---|
Title | Pholiota squarrosa lectin | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Lectin / Trimer / Fucose | ||||||
Function / homology | (3R)-butane-1,3-diol / Lectin (PhoSL) Function and homology information | ||||||
Biological species | Pholiota squarrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yamasaki, K. / Yamasaki, T. / Kubota, T. | ||||||
Citation | Journal: Glycobiology / Year: 2019 Title: Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL). Authors: Yamasaki, K. / Kubota, T. / Yamasaki, T. / Nagashima, I. / Shimizu, H. / Terada, R.I. / Nishigami, H. / Kang, J. / Tateno, M. / Tateno, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6a86.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6a86.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/6a86 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/6a86 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6a87C 5xzkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 4440.958 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Pholiota squarrosa (fungus) / References: UniProt: A0A384E107*PLUS #2: Chemical | ChemComp-BU4 / ( #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.8 M potassium-sodium phosphate (pH 7.0), 5% 1,3-butanediol |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2017 |
Radiation | 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: 28520 / % possible obs: 98.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.391 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XZK Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.012 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.127 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.655 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|