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Yorodumi- PDB-8i3p: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i3p | ||||||
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Title | crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one | ||||||
Components | Cytosine deaminase | ||||||
Keywords | HYDROLASE / metalloenzyme | ||||||
Function / homology | Function and homology information cytidine metabolic process / pyrimidine-containing compound salvage / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / 5-fluorocytosine deaminase activity / cytosine deaminase activity / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Qin, M.M. / Deng, H.Z. / Yao, L.S. | ||||||
Funding support | China, 1items
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Citation | Journal: To be published Title: crystal structure of yeast cytosine deaminase mutant yCD-RQ-1/8SAH in complex with (R)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one Authors: Qin, M.M. / Deng, H.Z. / Yao, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i3p.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i3p.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 8i3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/8i3p ftp://data.pdbj.org/pub/pdb/validation_reports/i3/8i3p | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22764.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: FCY1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12178, cytosine deaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 31.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.5 M Ammonium sulfate, 0.1 M Tris pH 8.5, 12% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→48.42 Å / Num. obs: 69899 / % possible obs: 85.6 % / Redundancy: 2.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.031 / Rrim(I) all: 0.053 / Χ2: 0.46 / Net I/σ(I): 9.5 / Num. measured all: 223856 |
Reflection shell | Resolution: 1.18→1.24 Å / % possible obs: 81.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.262 / Num. measured all: 27029 / Num. unique obs: 12501 / CC1/2: 0.902 / Rpim(I) all: 0.22 / Rrim(I) all: 0.344 / Χ2: 0.39 / Net I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→33.41 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.77 / Stereochemistry target values: ML
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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: 1.3→33.41 Å
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Refine LS restraints |
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LS refinement shell |
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