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Yorodumi- PDB-8vlk: Crystal structure of the yeast cytosine deaminase containing both... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vlk | |||||||||
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Title | Crystal structure of the yeast cytosine deaminase containing both open and closed active sites | |||||||||
Components | Cytosine deaminase | |||||||||
Keywords | ANTIFUNGAL PROTEIN / cytosine deaminase / resistance / heterodimer | |||||||||
Function / homology | Function and homology information cytidine metabolic process / pyrimidine-containing compound salvage / diaminohydroxyphosphoribosylaminopyrimidine deaminase activity / cytosine deaminase / : / cytosine deaminase activity / UMP salvage / cytosine metabolic process / zinc ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | |||||||||
Authors | Picard, M.-E. / Grenier, J. / Despres, P.C. / Dube, A.K. / Landry, C.R. / Shi, R. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Science / Year: 2024 Title: Compensatory mutations potentiate constructive neutral evolution by gene duplication Authors: Despres, P.C. / Dube, A.K. / Picard, M.-E. / Grenier, J. / Shi, R. / Landry, C.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vlk.cif.gz | 140.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vlk.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 8vlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/8vlk ftp://data.pdbj.org/pub/pdb/validation_reports/vl/8vlk | HTTPS FTP |
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-Related structure data
Related structure data | 8vljC 8vllC 8vlmC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17812.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FCY1, YPR062W, YP9499.17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12178, cytosine deaminase #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / #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: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6 Details: 0.2 M lithium sulfate, 0.1 M MES pH 6.0 and 20% PEG-4000, cryoprotected by the reservoir solution supplemented with 15% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.27899 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.27899 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→94.49 Å / Num. obs: 58759 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 12.2 / Num. measured all: 387827 |
Reflection shell | Resolution: 1.76→1.86 Å / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.883 / Num. measured all: 55282 / Num. unique obs: 8542 / CC1/2: 0.736 / Rpim(I) all: 0.41 / Rrim(I) all: 1.055 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→52.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.748 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.805 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→52.74 Å
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Refine LS restraints |
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