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Yorodumi- PDB-4lhn: Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lhn | ||||||
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Title | Structure of the N-terminal domain of the Flo1 adhesin (N-Flo1p) from the yeast Saccharomyces cerevisiae, in complex with calcium and mannose | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.12 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 | 4lhn.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lhn.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/4lhn ftp://data.pdbj.org/pub/pdb/validation_reports/lh/4lhn | HTTPS FTP |
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-Related structure data
Related structure data | 4lhkC 4lhlC 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: Sugar | ChemComp-MAN / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.78 Å3/Da / Density % sol: 55.74 % |
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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: 1 M NaCl, 15% v/v EtOH, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 16, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→15.37 Å / Num. all: 16718 / Num. obs: 16718 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.12→2.23 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2106 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XJQ Resolution: 2.12→15.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.088 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.154 / 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: 26.134 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→15.03 Å
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