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Yorodumi- PDB-4af9: Crystal Structure of Epithelial Adhesin 1 A domain (Epa1A) from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4af9 | |||||||||
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Title | Crystal Structure of Epithelial Adhesin 1 A domain (Epa1A) from Candida glabrata in complex with Galb1-3Glc | |||||||||
Components | EPA1P | |||||||||
Keywords | CELL ADHESION / LECTIN / TISSUE INVASION / PATHOGENICITY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | CANDIDA GLABRATA (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Maestre-Reyna, M. / Diderrich, R. / Veelders, M.S. / Eulenburg, G. / Kalugin, V. / Brueckner, S. / Keller, P. / Rupp, S. / Moesch, H.-U. / Essen, L.-O. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural Basis for Promiscuity and Specificity During Candida Glabrata Invasion of Host Epithelia. Authors: Maestre-Reyna, M. / Diderrich, R. / Veelders, M.S. / Eulenburg, G. / Kalugin, V. / Bruckner, S. / Keller, P. / Rupp, S. / Mosch, H. / Essen, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4af9.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4af9.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 4af9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/4af9 ftp://data.pdbj.org/pub/pdb/validation_reports/af/4af9 | HTTPS FTP |
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-Related structure data
Related structure data | 4afaC 4afbC 4afcC 4aslC 2xjpS 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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 29436.619 Da / Num. of mol.: 1 / Fragment: ADHESION DOMAIN (A DOMAIN), RESIDUES 31-271 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA GLABRATA (fungus) / Strain: CBS138 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): SHUFFLE T7 EXPRESS (C3029) / References: UniProt: Q6VBJ0 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 276 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | B-D-GALACTOSE (GAL): BUILDS GALB1-3GLC WITH GLUCOSE. ALPHA-D-GLUCOSE (GLC): BUILDS GALB1-3GLC WITH ...B-D-GALACTOSE (GAL): BUILDS GALB1-3GLC WITH GLUCOSE. ALPHA-D-GLUCOSE (GLC): BUILDS GALB1-3GLC WITH GALACTOSE. IS A MIXTURE OF ALPHA AND BETA GLUCOSE |
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Sequence details | WE WORKED WITH THE N-TERMINAL ADHESIVE DOMAIN OF EPA1A, WHILE Q6VBJ0 PRESENTS THE ENTIRE SEQUENCE. ...WE WORKED WITH THE N-TERMINAL ADHESIVE DOMAIN OF EPA1A, WHILE Q6VBJ0 PRESENTS THE ENTIRE SEQUENCE. WE USED Q6VBJ0 SEQUENCE NUMBERING THROUGHOUT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.75 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M MES PH 6.5, 0.2 M AMMONIUM SULFATE, 0.025 M LACTOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 24, 2009 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: DIAMOND AND GE FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.89 Å / Num. obs: 43249 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XJP Resolution: 1.5→19.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.557 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.008 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.89 Å
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Refine LS restraints |
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