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- PDB-5nnu: KSHV uracil-DNA glycosylase, product complex with dsDNA exhibitin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nnu | ||||||
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Title | KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping | ||||||
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![]() | HYDROLASE / Uracil-DNA glycosylase | ||||||
Function / homology | ![]() base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Earl, C. / Bagneris, C. / Barrett, T. / Savva, R. | ||||||
![]() | ![]() Title: A structurally conserved motif in gamma-herpesvirus uracil-DNA glycosylases elicits duplex nucleotide-flipping. Authors: Earl, C. / Bagneris, C. / Zeman, K. / Cole, A. / Barrett, T. / Savva, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.2 KB | Display | ![]() |
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PDB format | ![]() | 182 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.6 KB | Display | ![]() |
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Full document | ![]() | 495.9 KB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nn7C ![]() 5nnhC ![]() 2j8xS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3230.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: AAB: DNA abasic site / Source: (synth.) synthetic construct #2: Protein | Mass: 27226.174 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q76RG8, UniProt: F5HFA1*PLUS, uracil-DNA glycosylase #3: DNA chain | Mass: 3365.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 59.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate, 0.1 M magnesium acetate, 8% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→73.09 Å / Num. obs: 33476 / % possible obs: 100 % / Redundancy: 3.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.144 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.97→9.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4405 / CC1/2: 0.656 / Rpim(I) all: 0.65 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2J8X Resolution: 2.97→49.2 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.77 Å2 / Biso mean: 73.1692 Å2 / Biso min: 27.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.97→49.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.97→3.047 Å / Total num. of bins used: 20
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