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Yorodumi- PDB-6ygg: NADase from Aspergillus fumigatus complexed with a substrate anologue -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ygg | ||||||
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Title | NADase from Aspergillus fumigatus complexed with a substrate anologue | ||||||
Components | AfNADase | ||||||
Keywords | HYDROLASE / NAD+ glycohydrolase / NAD / Ca-binding / homodimer / glycoprotein / benzamide adenine dinucleotide | ||||||
Function / homology | Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin / : / NAD+ glycohydrolase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / extracellular region / metal ion binding / Chem-DQV / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA Function and homology information | ||||||
Biological species | Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Stromland, O. / Ziegler, M. / Kallio, J.P. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Discovery of fungal surface NADases predominantly present in pathogenic species. Authors: Stromland, O. / Kallio, J.P. / Pschibul, A. / Skoge, R.H. / Hardardottir, H.M. / Sverkeli, L.J. / Heinekamp, T. / Kniemeyer, O. / Migaud, M. / Makarov, M.V. / Gossmann, T.I. / Brakhage, A.A. / Ziegler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ygg.cif.gz | 226.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ygg.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ygg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/6ygg ftp://data.pdbj.org/pub/pdb/validation_reports/yg/6ygg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27680.092 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_6G14470 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4WL81 |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose #3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 4 types, 462 molecules
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-DQV / [( | #8: Water | ChemComp-HOH / | |
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-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: 2.53 Å3/Da / Density % sol: 51.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate, 0.3 M CaCl2 and 20-25% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91589 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.66 Å / Num. obs: 45536 / % possible obs: 98.52 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1426 / Net I/σ(I): 9.33 |
Reflection shell | Resolution: 1.85→1.916 Å / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 4447 / CC1/2: 0.513 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292105770 Resolution: 1.85→48.66 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7699 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→48.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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