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Yorodumi- PDB-1k70: The Structure of Escherichia coli Cytosine Deaminase bound to 4-H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k70 | |||||||||
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Title | The Structure of Escherichia coli Cytosine Deaminase bound to 4-Hydroxy-3,4-Dihydro-1H-Pyrimidin-2-one | |||||||||
Components | Cytosine Deaminase | |||||||||
Keywords | HYDROLASE / cytosine deaminase / alpha-beta barrel / hexamer / conformational change | |||||||||
Function / homology | Function and homology information cytosine catabolic process / isoguanine deaminase activity / cytosine deaminase / : / 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 / MAD / Resolution: 1.8 Å | |||||||||
Authors | Ireton, G.C. / McDermott, G. / Black, M.E. / Stoddard, B.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The structure of Escherichia coli cytosine deaminase. Authors: Ireton, G.C. / McDermott, G. / Black, M.E. / Stoddard, B.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k70.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k70.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1k70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k70_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 1k70_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 1k70_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 1k70_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k70 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k70 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | he biological assembly is a hexamer of three domain swapped dimers generated form the monomer in the asymmetric unit by the operations:-y,x-y,z;y-x,-x,z; y,x,-z;x-y,-y,-z and -x,y-x,z. |
-Components
#1: Protein | Mass: 47513.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25524, cytosine deaminase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-HPY / |
#4: 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: 57.84 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, magnesium chloride, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.7 / PH range high: 7.3 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2001 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 50003 / Num. obs: 50003 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 12.7 / % possible all: 92.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 51159 / Num. measured all: 331182 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 92.2 % / Mean I/σ(I) obs: 12.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 710238.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.0446 Å2 / ksol: 0.402847 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.177 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.273 |