+Open data
-Basic information
Entry | Database: PDB / ID: 5ysk | ||||||
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Title | SdeA mART-C domain EE/AA apo | ||||||
Components | Ubiquitinating/deubiquitinating enzyme SdeA | ||||||
Keywords | HYDROLASE / E3 ligase | ||||||
Function / homology | Function and homology information NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / host cell / nucleotidyltransferase activity ...NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / host cell / nucleotidyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein ubiquitination / nucleotide binding / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | ||||||
Authors | Kim, L. / Kwon, D.H. / Song, H.K. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila Authors: Kim, L. / Kwon, D.H. / Kim, B.H. / Kim, J. / Park, M.R. / Park, Z.Y. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ysk.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ysk.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ysk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ysk ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ysk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16923.611 Da / Num. of mol.: 4 / Mutation: E860A, E862A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: sdeA, lpg2157 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5ZTK4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jun 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.403→32.42 Å / Num. obs: 19830 / % possible obs: 97.99 % / Redundancy: 3.6 % / Net I/σ(I): 34.6762 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→32.42 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→32.42 Å
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Refine LS restraints |
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LS refinement shell |
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