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Yorodumi- PDB-6y9j: Crystal Structure of subtype-switched Epithelial Adhesin 1 to 9 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y9j | |||||||||
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Title | Crystal Structure of subtype-switched Epithelial Adhesin 1 to 9 A domain (Epa1-CBL2Epa9) from Candida glabrata in complex with beta-lactose | |||||||||
Components | Epa1p | |||||||||
Keywords | SUGAR BINDING PROTEIN / Epithelial adhesin | |||||||||
Function / homology | Function and homology information cell-abiotic substrate adhesion / adhesion of symbiont to host / fungal-type cell wall / cell adhesion molecule binding / carbohydrate binding / cell surface / metal ion binding Similarity search - Function | |||||||||
Biological species | Candida glabrata (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | |||||||||
Authors | Hoffmann, D. / Diderrich, R. / Kock, M. / Friederichs, S. / Reithofer, V. / Essen, L.-O. / Moesch, H.-U. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Functional reprogramming ofCandida glabrataepithelial adhesins: the role of conserved and variable structural motifs in ligand binding. Authors: Hoffmann, D. / Diderrich, R. / Reithofer, V. / Friederichs, S. / Kock, M. / Essen, L.O. / Mosch, H.U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y9j.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y9j.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 6y9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y9j_validation.pdf.gz | 826.4 KB | Display | wwPDB validaton report |
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Full document | 6y9j_full_validation.pdf.gz | 828.4 KB | Display | |
Data in XML | 6y9j_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 6y9j_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/6y9j ftp://data.pdbj.org/pub/pdb/validation_reports/y9/6y9j | HTTPS FTP |
-Related structure data
Related structure data | 6y98C 4aslS 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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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: 29445.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (fungus) / Gene: EPA1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6VBJ0, UniProt: Q6FUW5*PLUS |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
-Non-polymers , 4 types, 326 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.27 Å3/Da / Density % sol: 45.74 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES pH 6.5, 0.2 M ammonium sulfate, 25 % PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→34.545 Å / Num. obs: 107346 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.449 / Num. unique obs: 4801 / CC1/2: 0.425 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ASL Resolution: 1.1→34.545 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.84 Å2 / Biso mean: 20.6925 Å2 / Biso min: 9.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→34.545 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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