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Open data
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Basic information
Entry | Database: PDB / ID: 8i3n | ||||||
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Title | crystal structure of yeast cytosine deaminase mutant yCD-RQ | ||||||
![]() | Cytosine deaminase | ||||||
![]() | HYDROLASE / cytosine deaminase / mutant / 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 | ![]()
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![]() | ![]() Title: The crystal structure of rational designed yCD mutant yCD-RQ Authors: Qin, M.M. / Yao, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
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PDB format | ![]() | 107 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19982.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: FCY1 / Production host: ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-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 | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M ammounium acetate, 27%-29% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 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: 1.73→82.29 Å / Num. obs: 65362 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Χ2: 0.86 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.73→1.82 Å / % possible obs: 97.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.48 / Num. measured all: 25357 / Num. unique obs: 9660 / CC1/2: 0.867 / Rpim(I) all: 0.35 / Rrim(I) all: 0.597 / Χ2: 0.61 / Net I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→82.29 Å
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Refine LS restraints |
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LS refinement shell |
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