[English] 日本語
![](img/lk-miru.gif)
- PDB-4lhk: Structure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-F... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4lhk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the N-terminal domain of the Lg-Flo1 adhesin (N-Lg-Flo1p) from the yeast Saccharomyces pastorianus, in complex with calcium and alpha-1,2-mannobiose | |||||||||
![]() | Flocculin | |||||||||
![]() | CELL ADHESION / PA14 domain | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ielasi, F.S. / Willaert, R.G. | |||||||||
![]() | ![]() Title: Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. Authors: Goossens, K.V. / Ielasi, F.S. / Nookaew, I. / Stals, I. / Alonso-Sarduy, L. / Daenen, L. / Van Mulders, S.E. / Stassen, C. / van Eijsden, R.G. / Siewers, V. / Delvaux, F.R. / Kasas, S. / ...Authors: Goossens, K.V. / Ielasi, F.S. / Nookaew, I. / Stals, I. / Alonso-Sarduy, L. / Daenen, L. / Van Mulders, S.E. / Stassen, C. / van Eijsden, R.G. / Siewers, V. / Delvaux, F.R. / Kasas, S. / Nielsen, J. / Devreese, B. / Willaert, R.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: The mannose-specific lectin domains of Flo1p from Saccharomyces cerevisiae and Lg-Flo1p from S. pastorianus: crystallization and preliminary X-ray diffraction analysis of the adhesin-carbohydrate complexes. Authors: Ielasi, F.S. / Goyal, P. / Sleutel, M. / Wohlkonig, A. / Willaert, R.G. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 195.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 155.3 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 | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lhlC ![]() 4lhnC ![]() 2xjqS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26418.146 Da / Num. of mol.: 2 / Fragment: N-terminal domain,UNP residues 23-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CBS1513 / Gene: Lg-FLO1 / Plasmid: pET-21b(+) / Production host: ![]() ![]() #2: Polysaccharide | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | UNIPROT ENTRY B3IUB3 REPORTS A PROLINE AT POSITION 58, WHILE THE AUTHORS HAVE CONFIRMED A GLUTAMINE ...UNIPROT ENTRY B3IUB3 REPORTS A PROLINE AT POSITION 58, WHILE THE AUTHORS HAVE CONFIRMED A GLUTAMINE AT THAT POSITION AND HENCE Q 58 IS A NATURAL VARIANT. THE AUTHORS SAY THAT B3IUB3 ENTRY IN UNIPROT IS NOT COMPLETE AND IT STOPS AT AA 213. FOR AA 214-247, THE SEQUENCE REPORTED HERE IS IDENTICAL TO THE ONE REPORTED FOR UNIPROT B3IUA8. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2 Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M ...Details: Protein solution: 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 10 mM CaCl2 Crystallization condition: 0.1 M amino acids (L-Na-glutamate, DL-alanine, glycine, DL-lysine-HCl, DL-serine), 0.1 M imidazole-MES pH 6.5, 30% w/v PEG 550 MME - PEG 20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2012 |
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→38.54 Å / Num. all: 44852 / Num. obs: 44852 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2430 / % possible all: 96 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XJQ Resolution: 1.73→35.13 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.788 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.101 / 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: 22.116 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→35.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|