+Open data
-Basic information
Entry | Database: PDB / ID: 5o9r | |||||||||
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Title | Crystal structure of ScGas2 in complex with compound 9 | |||||||||
Components | 1,3-beta-glucanosyltransferase GAS2 | |||||||||
Keywords | TRANSFERASE / Aspergillus fumigatus / AfGel4 / ScGas2 / transglycosylases / glucanosyltransferases / cell wall remodeling / fungal cell wall | |||||||||
Function / homology | Function and homology information 1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / fungal-type cell wall beta-glucan biosynthetic process / ascospore wall assembly / fungal-type cell wall organization / fungal-type vacuole / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Delso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / Van Aalten, D. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R. | |||||||||
Citation | Journal: ChemMedChem / Year: 2018 Title: Inhibitors against Fungal Cell Wall Remodeling Enzymes. Authors: Delso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / van Aalten, D.M.F. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o9r.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o9r.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 5o9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o9r_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5o9r_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5o9r_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 5o9r_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9r ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9r | HTTPS FTP |
-Related structure data
Related structure data | 5o9oC 5o9pC 5o9qC 5o9yC 5oa2C 5oa6C 2w62S 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 62426.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: GAS2, YLR343W, L8300.5 / Production host: Komagataella pastoris (fungus) References: UniProt: Q06135, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 340 molecules
#3: Chemical | ChemComp-9PK / ( | ||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | #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: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3500, ammonium sulfate, BIS-Tris pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→150.44 Å / Num. obs: 60003 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W62 Resolution: 1.7→150.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.928 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.094 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.376 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→150.44 Å
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Refine LS restraints |
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