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- PDB-6ajd: Crystal structure of a monometallic dihydropyrimidinase from Pseu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ajd | ||||||
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Title | Crystal structure of a monometallic dihydropyrimidinase from Pseudomonas aeruginosa PAO1 reveals no lysine carbamylation within the active site | ||||||
![]() | 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. / Huang, C.Y. | ||||||
![]() | ![]() Title: Crystal structures of monometallic dihydropyrimidinase and the human dihydroorotase domain K1556A mutant reveal no lysine carbamylation within the active site Authors: Cheng, J.H. / Huang, Y.H. / Lin, J.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 | ![]() | 196.7 KB | Display | ![]() |
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PDB format | ![]() | 155.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 35 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ynzC ![]() 5e5cS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 53101.715 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25%PEG4000, 100mM Tris-HCl pH8.5, 200mM Calcium Chloride |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.223→30 Å / Num. obs: 54478 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.223→2.31 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 5383 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E5C Resolution: 2.223→29.277 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.223→29.277 Å
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Refine LS restraints |
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LS refinement shell |
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