+Open data
-Basic information
Entry | Database: PDB / ID: 6lfu | |||||||||
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Title | Poa1p F152A mutant in complex with ADP-ribose | |||||||||
Components | ADP-ribose 1''-phosphate phosphatase | |||||||||
Keywords | HYDROLASE / deacetylase / macro domain | |||||||||
Function / homology | Function and homology information ADP-ribosyl-[dinitrogen reductase] hydrolase activity / tRNA splicing, via endonucleolytic cleavage and ligation / ADP-ribose 1''-phosphate phosphatase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / phosphatase activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.123 Å | |||||||||
Authors | Chiu, Y.C. / Hsu, C.H. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Acs Catalysis / Year: 2021 Title: Expanding the Substrate Specificity of Macro Domains toward 3''-Isomer of O-Acetyl-ADP-ribose Authors: Chiu, Y.C. / Tseng, M.C. / Hsu, C.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lfu.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lfu.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lfu_validation.pdf.gz | 945.2 KB | Display | wwPDB validaton report |
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Full document | 6lfu_full_validation.pdf.gz | 957 KB | Display | |
Data in XML | 6lfu_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6lfu_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/6lfu ftp://data.pdbj.org/pub/pdb/validation_reports/lf/6lfu | HTTPS FTP |
-Related structure data
Related structure data | 6lfqSC 6lfrC 6lfsC 6lftC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20167.994 Da / Num. of mol.: 2 / Mutation: F152A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: POA1, YBR022W, YBR0304 / Production host: Escherichia coli (E. coli) References: UniProt: P38218, ADP-ribose 1''-phosphate phosphatase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds #2: Chemical | 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: 2.2 Å3/Da / Density % sol: 44.11 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: Citric acid, PEG 3350, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.123→24.884 Å / Num. obs: 5850 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.985 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 3.123→3.4361 Å / CC1/2: 0.953 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LFQ Resolution: 3.123→24.884 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.92 Å2 / Biso mean: 50.6133 Å2 / Biso min: 19.33 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.123→24.884 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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