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Open data
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Basic information
Entry | Database: PDB / ID: 1ugi | ||||||
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Title | URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN | ||||||
![]() | URACIL-DNA GLYCOSYLASE INHIBITOR | ||||||
![]() | HYDROLASE INHIBITOR / PROTEIN MIMICRY OF DNA / PROTEIN INHIBITOR | ||||||
Function / homology | Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / IMIDAZOLE / Uracil-DNA glycosylase inhibitor![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Putnam, C.D. / Arvai, A.S. / Mol, C.D. / Tainer, J.A. | ||||||
![]() | ![]() Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase Authors: Putnam, C.D. / Shroyer, M.J. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157 KB | Display | ![]() |
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PDB format | ![]() | 126.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 499.6 KB | Display | ![]() |
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Full document | ![]() | 515.9 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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8 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 9482.674 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-IMD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.2 / Details: pH 8.2, temperature 277K | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 95452 / % possible obs: 86.7 % / Redundancy: 2.3 % / Rsym value: 0.064 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.368 / % possible all: 86.5 |
Reflection | *PLUS Num. measured all: 221922 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 86.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ORTHORHOMBIC CRYSTAL FORM OF FREE UGI Resolution: 1.55→20 Å / Num. parameters: 24407 / Num. restraintsaints: 22880 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: BABINET'S PRINCIPLE SCALING | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 24 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.222 / Rfactor Rfree: 0.289 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.55 Å / Lowest resolution: 1.62 Å / Rfactor Rfree: 0.348 / Num. reflection obs: 9225 / Rfactor obs: 0.329 |