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Yorodumi- PDB-4le8: Structure of the Als3 adhesin from Candida albicans, residues 1-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4le8 | ||||||
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Title | Structure of the Als3 adhesin from Candida albicans, residues 1-299 (mature sequence) | ||||||
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 / 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 ...high molecular weight kininogen binding / reductive iron assimilation / cell adhesion involved in multi-species biofilm formation / 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 / symbiont entry into host / cell adhesion involved in single-species biofilm formation / 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: 1.75 Å | ||||||
Authors | Lin, J. / Garnett, J.A. / Cota, E. | ||||||
Citation | Journal: To be Published Title: The peptide binding mechanism of Als3 mediates early attachment of Candida albicans to host cells Authors: Lin, J. / Garnett, J.A. / Cota, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4le8.cif.gz | 246.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4le8.ent.gz | 199.5 KB | Display | PDB format |
PDBx/mmJSON format | 4le8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/4le8 ftp://data.pdbj.org/pub/pdb/validation_reports/le/4le8 | HTTPS FTP |
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-Related structure data
Related structure data | 2y7nS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 0 - 299 / Label seq-ID: 1 - 300
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-Components
#1: Protein | Mass: 32395.850 Da / Num. of mol.: 2 Fragment: sNT-Als3 (truncated N-terminal domain, UNP residues 18-316) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: Candida albicans / Gene: ALD8, ALS3 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 SHuffle / References: UniProt: O74623, UniProt: Q59L12*PLUS #2: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 4 Details: 1.0 M lithium chloride, 0.1 M sodium citrate, pH 4.0, 20% w/v PEG6000, VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2011 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.75→71.56 Å / Num. obs: 55086 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 9.816 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.4 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3666 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y7N Resolution: 1.75→71.56 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.865 / SU B: 6.947 / SU ML: 0.132 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.041 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 20.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→71.56 Å
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Refine LS restraints |
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