+Open data
-Basic information
Entry | Database: PDB / ID: 6ygf | ||||||
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Title | NADase from Aspergillus fumigatus with trapped reaction products | ||||||
Components | AfNADase | ||||||
Keywords | HYDROLASE / NAD+ glycohydrolase / NAD / Ca-binding / homodimer / glycoprotein / nicotinamide / adenosine diphosphate ribose | ||||||
Function / homology | Function and homology information : / NAD+ glycohydrolase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 6ygf.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ygf.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 6ygf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/6ygf ftp://data.pdbj.org/pub/pdb/validation_reports/yg/6ygf | 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 BA
#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 , 4 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: 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 | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 5 types, 567 molecules
#6: Chemical | #7: Chemical | #8: Chemical | ChemComp-NCA / | #9: Chemical | ChemComp-AR6 / [( | #10: 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: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.04 M Potassium phosphate monobasic, 16% PEG 8000 and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→85.9 Å / Num. obs: 68236 / % possible obs: 99.74 % / Redundancy: 2 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02465 / Net I/σ(I): 15.17 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 6579 / CC1/2: 0.477 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292105770 Resolution: 1.7→85.9 Å / SU ML: 0.2258 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8257
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→85.9 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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