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Yorodumi- PDB-4coy: Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4coy | |||||||||
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Title | Crystal Structure of Epithelial Adhesin 6 A domain (Epa6A) from Candida glabrata in complex with Galb1-4GlcNAc | |||||||||
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: 1.8 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 | 4coy.cif.gz | 115 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4coy.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 4coy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4coy_validation.pdf.gz | 775.5 KB | Display | wwPDB validaton report |
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Full document | 4coy_full_validation.pdf.gz | 776.4 KB | Display | |
Data in XML | 4coy_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 4coy_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4coy ftp://data.pdbj.org/pub/pdb/validation_reports/co/4coy | HTTPS FTP |
-Related structure data
Related structure data | 4couC 4covC 4cowC 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
#1: Protein | Mass: 28515.475 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: CBS 138 / 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)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ACT / |
#5: 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: 2.42 Å3/Da / Density % sol: 49.16 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.01 M SODIUM ACETATE PH4.6, 30% PEG 4000, 0.2 M AMMONIUM ACETATE, 0.05 M LACTOSE, 291 K, VAPOR DIFFUSION IN SITTING DROP, SOAKED WITH GALB1-4GLCNAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.58 Å / Num. obs: 27537 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRUNED VERSION OF PDB ENTRY 4AF9 Resolution: 1.8→41.58 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.793 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / 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: 16.266 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.58 Å
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