+Open data
-Basic information
Entry | Database: PDB / ID: 6lye | |||||||||
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Title | Crystal Structure of mimivirus UNG Y322F in complex with UGI | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/INHIBITOR / UDG / UNG / uracil DNA glycosylase / UGI / DNA BINDING PROTEIN-INHIBITOR complex | |||||||||
Function / homology | Function and homology information uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / base-excision repair Similarity search - Function | |||||||||
Biological species | Acanthamoeba polyphaga mimivirus Bacillus phage PBS2 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Pathak, D. / Kwon, E. / Kim, D.Y. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Selective interactions between mimivirus uracil-DNA glycosylase and inhibitory proteins determined by a single amino acid. Authors: Pathak, D. / Kwon, E. / Kim, D.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lye.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lye.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/6lye ftp://data.pdbj.org/pub/pdb/validation_reports/ly/6lye | HTTPS FTP |
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-Related structure data
Related structure data | 6lydC 5x55S 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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Unit cell |
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-Components
#1: Protein | Mass: 31831.734 Da / Num. of mol.: 1 / Mutation: Y322F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: UNG, MIMI_L249 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5UPT2, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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#2: Protein | Mass: 9351.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage PBS2 (virus) / Gene: UGI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14739 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.14 % |
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Crystal grow | Temperature: 295 K / Method: batch mode Details: 16.75% (v/v) PEG3350, 8% (v/v) PEG400, and 0.1 M sodium acetate/acetic acid pH 5.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.34 |
Reflection | Resolution: 3.1→45.133 Å / Num. obs: 9163 / % possible obs: 97.6 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.1→3.31 Å / Rmerge(I) obs: 0.604 / Num. unique obs: 1685 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X55 Resolution: 3.1→45.133 Å / Cross valid method: THROUGHOUT / σ(F): 79.49 / Phase error: 25 / Stereochemistry target values: TWIN_LSQ_F
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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 max: 153.15 Å2 / Biso mean: 75.172 Å2 / Biso min: 39.46 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→45.133 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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