+Open data
-Basic information
Entry | Database: PDB / ID: 6lfq | |||||||||
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Title | Crystal structure of Poa1p in apo form | |||||||||
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: 2.359 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 | 6lfq.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lfq.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lfq_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 6lfq_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 6lfq_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6lfq_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/6lfq ftp://data.pdbj.org/pub/pdb/validation_reports/lf/6lfq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20244.090 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.52 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: HEPES sodium, Lithium sulfate monohydrate, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.359→29.806 Å / Num. obs: 6209 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.971 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.359→2.444 Å / CC1/2: 0.911 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.359→29.806 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.16 Å2 / Biso mean: 29.5345 Å2 / Biso min: 8.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.359→29.806 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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