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Open data
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Basic information
Entry | Database: PDB / ID: 1uaq | ||||||
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Title | The crystal structure of yeast cytosine deaminase | ||||||
![]() | cytosine deaminase | ||||||
![]() | HYDROLASE / alpha-beta-alpha | ||||||
Function / homology | ![]() cytidine metabolic process / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / pyrimidine-containing compound salvage / : / cytosine deaminase activity / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ko, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H. | ||||||
![]() | ![]() Title: Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution Authors: Ko, T.-P. / Lin, J.-J. / Hu, C.-Y. / Hsu, Y.-H. / Wang, A.H.-J. / Liaw, S.-H. #1: ![]() Title: Crystallization and preliminary crystallographic analysis of yeast cytosine deaminase Authors: Hsu, Y.-H. / Hu, C.-Y. / Lin, J.-J. / Liaw, S.-H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.4 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 17530.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: fcy1 / Plasmid: pET-6H / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.26 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: isopropanol, PEG4000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Hsu, Y.-H., (2003) Acta Crystallogr., Sect.D, 59, 950. | ||||||||||||||||||||||||||||||||||||
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: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2002 |
Radiation | Monochromator: the rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 42187 / Num. obs: 42187 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.057 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3945 / Rsym value: 0.297 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 277542 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 91.2 % / Num. unique obs: 3945 / Num. measured obs: 18894 / Rmerge(I) obs: 0.338 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters |
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Refine analyze | Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→23.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å /
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.6 Å / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.268 / Num. reflection obs: 3157 |