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Open data
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Basic information
Entry | Database: PDB / ID: 6lyd | |||||||||
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Title | Crystal Structure of mimivirus UNG Y322L in complex with UGI | |||||||||
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![]() | DNA BINDING PROTEIN/INHIBITOR / UDG / UNG / uracil DNA glycosylase / UGI / DNA BINDING PROTEIN-INHIBITOR complex | |||||||||
Function / homology | ![]() base-excision repair, AP site formation via deaminated base removal / uracil DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pathak, D. / Kwon, E. / Kim, D.Y. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 441.4 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lyeC ![]() 5x55S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31797.719 Da / Num. of mol.: 1 / Mutation: Y322L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.05 % |
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Crystal grow | Temperature: 295 K / Method: batch mode Details: 10% PEG 8000 (v/v), 40 mM potassium phosphate monobasic, 20% glycerol (v/v), and 0.2 uL of 5% ethyl acetate (v/v) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 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 | Resolution: 2.598→50 Å / Num. obs: 15494 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.458 / Num. unique obs: 770 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X55 Resolution: 2.598→32.053 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.29 / Stereochemistry target values: ML
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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: 115.93 Å2 / Biso mean: 42.7332 Å2 / Biso min: 21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.598→32.053 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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