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- PDB-6klk: Crystal structure of the Pseudomonas aeruginosa dihydropyrimidina... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6klk | ||||||
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Title | Crystal structure of the Pseudomonas aeruginosa dihydropyrimidinase complexed with 5-FU | ||||||
![]() | D-hydantoinase/dihydropyrimidinase | ||||||
![]() | HYDROLASE / dihydropyrimidinase | ||||||
Function / homology | ![]() dihydropyrimidinase / dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, Y.H. / Chen, I.C. / Huang, C.Y. | ||||||
![]() | ![]() Title: Crystal structure of dihydropyrimidinase in complex with anticancer drug 5-fluorouracil. Authors: Huang, Y.H. / Ning, Z.J. / Huang, C.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.6 KB | Display | ![]() |
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PDB format | ![]() | 161.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 58.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e5cS S: Starting model for refinement |
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Similar structure data |
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Links
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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: 52315.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: dht, PA0441 / Production host: ![]() ![]() #2: Chemical | ChemComp-URF / | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 18%PEG8000, 100mM HEPES pH7.5, 200mM Calcium Acetate |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.759→30 Å / Num. obs: 114045 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.759→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.471 / Num. unique obs: 11296 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E5C Resolution: 1.759→27.833 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.96 Å2 / Biso mean: 23.187 Å2 / Biso min: 10.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.759→27.833 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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