[English] 日本語
Yorodumi- PDB-1rak: Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rak | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bacterial cytosine deaminase D314S mutant bound to 5-fluoro-4-(S)-hydroxyl-3,4-dihydropyrimidine. | |||||||||
Components | Cytosine deaminase | |||||||||
Keywords | HYDROLASE / CYTOSINE DEAMINASE / ALPHA-BETA BARREL / HEXAMER / CONFORMATIONAL CHANGE / D314S mutant | |||||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å | |||||||||
Authors | Mahan, S.D. / Ireton, G.C. / Stoddard, B.L. / Black, M.E. | |||||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2004 Title: Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy. Authors: Mahan, S.D. / Ireton, G.C. / Knoeber, C. / Stoddard, B.L. / Black, M.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rak.cif.gz | 109 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rak.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/1rak ftp://data.pdbj.org/pub/pdb/validation_reports/ra/1rak | HTTPS FTP |
---|
-Related structure data
Related structure data | 1r9xC 1r9yC 1r9zC 1ra0C 1ra5C 1k70S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6|||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||
Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: y,x,-z;y,y-x,-x,z;y,x,-z;x-y,-y,-z;-x,y-x,-z |
-Components
#1: Protein | Mass: 47831.988 Da / Num. of mol.: 1 / Mutation: D314S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CODA, B0337 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIL / References: UniProt: P25524, cytosine deaminase |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-FPY / ( |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
---|---|
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 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2003 |
Radiation | Monochromator: double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→20 Å / Num. all: 130301 / Num. obs: 126518 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.32→1.36 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.5 / % possible all: 95.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1K70 Resolution: 1.32→19.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 247101.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3438 Å2 / ksol: 0.384055 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→19.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.32→1.4 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|