[English] 日本語
![](img/lk-miru.gif)
- PDB-8i3o: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8i3o | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH | ||||||
![]() | Cytosine deaminase | ||||||
![]() | HYDROLASE / metalloenzyme | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Qin, M.M. / Yao, L.S. / Deng, H.Z. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH Authors: Qin, M.M. / Yao, L.S. / Deng, H.Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 254.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 202.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20955.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288c / Gene: FCY1 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.46 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15M ammounium acetate, 25%-29% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→60.77 Å / Num. obs: 41979 / % possible obs: 97.1 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Rrim(I) all: 0.105 / Χ2: 0.89 / Net I/σ(I): 10 / Num. measured all: 479992 |
Reflection shell | Resolution: 1.64→1.73 Å / % possible obs: 97.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.875 / Num. measured all: 72568 / Num. unique obs: 11096 / CC1/2: 0.882 / Rpim(I) all: 0.37 / Rrim(I) all: 0.951 / Χ2: 0.74 / Net I/σ(I) obs: 2.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→34.67 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.5669 Å / Origin y: -20.5816 Å / Origin z: -16.2712 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |