+Open data
-Basic information
Entry | Database: PDB / ID: 1k6w | ||||||
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Title | The Structure of Escherichia coli Cytosine Deaminase | ||||||
Components | Cytosine Deaminase | ||||||
Keywords | HYDROLASE / cytosine deaminase / alpha-beta barrel / hexamer / domain swap | ||||||
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 / SYNCHROTRON / MAD / Resolution: 1.75 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 | 1k6w.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k6w.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k6w_validation.pdf.gz | 413.8 KB | Display | wwPDB validaton report |
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Full document | 1k6w_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 1k6w_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 1k6w_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/1k6w ftp://data.pdbj.org/pub/pdb/validation_reports/k6/1k6w | 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 | The biological assembly is a hexamer of three domain swapped dimers generated from 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 / 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: 2.89 Å3/Da / Density % sol: 57.51 % | |||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.011 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2000 |
Radiation | Monochromator: Double cyrstal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 55446 / Num. obs: 55446 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.7 |
Reflection shell | Resolution: 1.75→1.86 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 26.8 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 55774 / Num. measured all: 362081 |
Reflection shell | *PLUS Lowest resolution: 1.79 Å / % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 231001.93 / 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: 57.1485 Å2 / ksol: 0.4184 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.009 / 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 / Num. reflection obs: 55695 / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.156 / Rfactor Rfree: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.187 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.156 |