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- PDB-4eug: 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: 4eug | ||||||
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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) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiao, G. / Tordova, M. / Drohat, A.C. / Jagadeesh, J. / Stivers, J.T. / Gilliland, G.L. | ||||||
![]() | ![]() Title: Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187. Authors: Drohat, A.C. / Xiao, G. / Tordova, M. / Jagadeesh, J. / Pankiewicz, K.W. / Watanabe, K.A. / Gilliland, G.L. / Stivers, J.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.9 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3eugS 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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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: 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: Xiao, G., (1999) Proteins Struct.Funct.Genet., 35, 13. | |||||||||||||||||||||||||
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: CCD / Date: Jul 15, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.4→99 Å / Num. obs: 77493 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3EUG Resolution: 1.4→99 Å / Num. parameters: 8359 / Num. restraintsaints: 7437 / 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: 1.4→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): 2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.028 |