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Yorodumi- PDB-4cou: Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cou | |||||||||
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Title | Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Lactose | |||||||||
Components | EPITHELIAL ADHESIN 6 | |||||||||
Keywords | CELL ADHESION / LECTIN / TISSUE INVASION / PATHOGENICITY | |||||||||
Function / homology | Function and homology information cell-abiotic substrate adhesion / single-species biofilm formation on inanimate substrate / fungal biofilm matrix / adhesion of symbiont to host / fungal-type cell wall / carbohydrate binding / cell surface / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | CANDIDA GLABRATA (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Kock, M. / Maestre-Reyna, M. / Diderrich, R. / Moesch, H.-U. / Essen, L.-O. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Hotspots Determine Functional Diversity of the Candida Glabrata Epithelial Adhesin Family Authors: Diderrich, R. / Kock, M. / Maestre-Reyna, M. / Rupp, S. / Essen, L.-O. / Moesch, H.-U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cou.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cou.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4cou ftp://data.pdbj.org/pub/pdb/validation_reports/co/4cou | HTTPS FTP |
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-Related structure data
Related structure data | 4covC 4cowC 4coyC 4cozC 4d3wC 4af9S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 29937.945 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 26-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS138 / Plasmid: PET28A / Production host: ESCHERICHIA COLI B (bacteria) / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6FX55 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
-Non-polymers , 4 types, 248 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-GOL / |
#6: 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: 2.24 Å3/Da / Density % sol: 45.14 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.08 M SODIUM ACETATE PH:4.6, 1.6 M AMMONIUM SULFATE, 20% GLYCEROL, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH MARMOSAIC 255 MM / Detector: CCD / Date: Sep 16, 2012 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→28.77 Å / Num. obs: 45573 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.48→1.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRUNED VERSION OF PDB ENTRY 4AF9 Resolution: 1.48→26.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.189 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.056 / 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: 19.167 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→26.5 Å
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Refine LS restraints |
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