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Yorodumi- PDB-4lhl: Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lhl | ||||||
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Title | Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) from the yeast Saccharomyces cerevisiae | ||||||
Components | Flocculation protein FLO1 | ||||||
Keywords | CELL ADHESION / PA14 domain | ||||||
Function / homology | Function and homology information flocculation / fungal-type cell wall / D-mannose binding / side of membrane / cell periphery / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Ielasi, F.S. / Willaert, R.G. | ||||||
Citation | Journal: MBio / Year: 2015 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lhl.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lhl.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/4lhl ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lhl | HTTPS FTP |
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-Related structure data
Related structure data | 4lhkC 4lhnC 2xjqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28462.291 Da / Num. of mol.: 1 / Fragment: N-terminal domain,UNP residues 23-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: BY4742 / Gene: FLO1, FLO2, FLO4, FLO8, YAR050W / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 (DE3) / References: UniProt: P32768 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein solution: 50 mM sodium acetate pH 5, 150 mM NaCl, 10 mM CaCl2 Crystallization condition: 2 M NaCl, 10% v/v EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2013 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→40.39 Å / Num. all: 56735 / Num. obs: 56735 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 3 / Num. unique all: 4114 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XJQ Resolution: 1.43→40.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.432 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.43→40.38 Å
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