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Yorodumi- PDB-4lee: Structure of the Als3 adhesin from Candida albicans, residues 1-3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lee | ||||||
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Title | Structure of the Als3 adhesin from Candida albicans, residues 1-313 (mature sequence), triple mutant in the binding cavity: K59M, A116V, Y301F | ||||||
Components | Agglutinin-like protein 3 | ||||||
Keywords | CELL ADHESION / adhesin / peptide binding protein / biofilm formation / cellular adhesion / peptides / cell surface | ||||||
Function / homology | Function and homology information high molecular weight kininogen binding / reductive iron assimilation / cell adhesion involved in multi-species biofilm formation / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / yeast-form cell wall / cell adhesion involved in biofilm formation / single-species biofilm formation on inanimate substrate / hyphal cell wall / adhesion of symbiont to host ...high molecular weight kininogen binding / reductive iron assimilation / cell adhesion involved in multi-species biofilm formation / biological process involved in symbiotic interaction / filamentous growth of a population of unicellular organisms / yeast-form cell wall / cell adhesion involved in biofilm formation / single-species biofilm formation on inanimate substrate / hyphal cell wall / adhesion of symbiont to host / fungal-type cell wall / cell adhesion involved in single-species biofilm formation / symbiont entry into host / intracellular copper ion homeostasis / side of membrane / cell adhesion molecule binding / cell-cell adhesion / endocytosis / extracellular vesicle / cell adhesion / cell surface / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lin, J. / Garnett, J.A. / Cota, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: The Peptide-binding Cavity Is Essential for Als3-mediated Adhesion of Candida albicans to Human Cells. Authors: Lin, J. / Oh, S.H. / Jones, R. / Garnett, J.A. / Salgado, P.S. / Rusnakova, S. / Matthews, S.J. / Hoyer, L.L. / Cota, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lee.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lee.ent.gz | 189.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4lee ftp://data.pdbj.org/pub/pdb/validation_reports/le/4lee | HTTPS FTP |
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-Related structure data
Related structure data | 4lebC 4le8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 0 - 312 / Label seq-ID: 1 - 313
NCS ensembles :
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-Components
#1: Protein | Mass: 33709.297 Da / Num. of mol.: 4 / Fragment: NT-Als3 (N-terminal domain, UNP residues 18-330) / Mutation: K59M, A116V, Y301F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: ALD8, ALS3 / Plasmid: PET32 XA/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 SHuffle / References: UniProt: O74623, UniProt: Q59L12*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.91 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8 Details: 25% w/v PEG4000, 30% v/v ethylene glycol, pH 8, VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å | |||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3→48.33 Å / Num. obs: 32262 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 61.783 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.6 | |||||||||||||||
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2312 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LE8 Resolution: 3→48.33 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.876 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 44.574 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.33 Å
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Refine LS restraints |
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