+Open data
-Basic information
Entry | Database: PDB / ID: 6eke | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of a Pholiota squarrosa lectin unliganded | ||||||
Components | lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | metal ion binding / ACETATE ION / 1,4-BUTANEDIOL / Lectin Function and homology information | ||||||
Biological species | Pholiota squarrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Cabanettes, A. / Varrot, A. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Recognition of Complex Core-Fucosylated N-Glycans by a Mini Lectin. Authors: Cabanettes, A. / Perkams, L. / Spies, C. / Unverzagt, C. / Varrot, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6eke.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6eke.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 6eke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eke_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6eke_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 6eke_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 6eke_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/6eke ftp://data.pdbj.org/pub/pdb/validation_reports/ek/6eke | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 4711.271 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pholiota squarrosa (fungus) / Plasmid: pET39a-TEV-PhosL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A3B6UEU4*PLUS #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.37 % / Description: triangle |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7 Details: 18% butane1,4diol, 300mM zinc acetate, 100 mM imidazole ph 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.984 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.83 Å / Num. obs: 12666 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.041 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3 / Num. unique obs: 644 / CC1/2: 0.892 / Rpim(I) all: 0.304 / % possible all: 97.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.7→33.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.396 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.112 / 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: 25.07 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→33.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|