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- PDB-2eug: CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2eug | ||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE AND ITS COMPLEXES WITH URACIL AND GLYCEROL: STRUCTURE AND GLYCOSYLASE MECHANISM REVISITED | ||||||
![]() | PROTEIN (GLYCOSYLASE) | ||||||
![]() | HYDROLASE / GLYCOSYLASE | ||||||
Function / homology | ![]() base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xiao, G. / Tordova, M. / Jagadeesh, J. / Drohat, A.C. / Stivers, J.T. / Gilliland, G.L. | ||||||
![]() | ![]() Title: Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited. Authors: Xiao, G. / Tordova, M. / Jagadeesh, J. / Drohat, A.C. / Stivers, J.T. / Gilliland, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.4 KB | Display | ![]() |
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PDB format | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1eugSC ![]() 3eugC ![]() 5eugC 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: 25681.107 Da / Num. of mol.: 1 / Mutation: Y19H Source method: isolated from a genetically manipulated source Details: THE PROTEIN IS COMPLEXED WITH URACIL / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-URA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN CONCENTRATION 14.9 MG/ML, 0.2 M SODIUM ACETATE, 30% PEG4000, 0.1 M TRIS BUFFER, PH 8.5 USING HANGING DROP AT 293K. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER / Detector: AREA DETECTOR / Date: Aug 15, 1997 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→99 Å / Num. obs: 32361 / % possible obs: 97 % / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.4 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EUG Resolution: 1.5→99 Å / Num. parameters: 8464 / Num. restraintsaints: 7489 / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2086 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→99 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 99 Å / σ(F): 1 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.026 |