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- PDB-5eug: CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5eug | ||||||
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Title | CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT H187Q OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE: CRYSTAL STRUCTURES OF MUTANT H187Q AND ITS URACIL COMPLEX | ||||||
![]() | 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. / Drohat, A.C. / Jagadeesh, J. / 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 | ![]() | 62.4 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.6 KB | Display | ![]() |
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Full document | ![]() | 411.3 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 11.1 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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Unit cell |
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Components
#1: Protein | Mass: 25696.117 Da / Num. of mol.: 1 / Mutation: H187Q Source method: isolated from a genetically manipulated source 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 dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||
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: Sep 15, 1998 |
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: 1.6→99 Å / Num. obs: 126877 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.6→1.658 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 58 |
Reflection shell | *PLUS % possible obs: 58 % |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.6→99 Å / Num. parameters: 8307 / Num. restraintsaints: 7469 / σ(F): 2 / 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: 2087 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→99 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.024 |