+Open data
-Basic information
Entry | Database: PDB / ID: 3g77 | ||||||
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Title | Bacterial cytosine deaminase V152A/F316C/D317G mutant | ||||||
Components | Cytosine deaminase | ||||||
Keywords | HYDROLASE / cytosine deaminase / protein engineering / Cytosine metabolism / Iron / Metal-binding | ||||||
Function / homology | Function and homology information cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / 5-fluorocytosine deaminase activity / cytosine deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / ferrous iron binding / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Stoddard, B. / Zhao, L. | ||||||
Citation | Journal: Cancer Res. / Year: 2009 Title: Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo. Authors: Fuchita, M. / Ardiani, A. / Zhao, L. / Serve, K. / Stoddard, B.L. / Black, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g77.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g77.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 3g77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g77 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g77 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47068.191 Da / Num. of mol.: 1 / Mutation: V152A, F316C, D317G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: codA, b0337, JW0328 / Production host: Escherichia coli (E. coli) / References: UniProt: P25524, cytosine deaminase |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 100 mM magnesium chloride, 10 mM 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.48 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 13, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.48 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→87.71 Å / Num. obs: 50592 / % possible obs: 98.7 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.033 / Χ2: 0.93 / Scaling rejects: 1535 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.8→37.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 1.621 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.1 / 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 max: 37.05 Å2 / Biso mean: 11.469 Å2 / Biso min: 2.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.13 Å
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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