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- PDB-4lcr: The crystal structure of di-Zn dihydropyrimidinase in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lcr | ||||||
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Title | The crystal structure of di-Zn dihydropyrimidinase in complex with NCBA | ||||||
![]() | Chromosome 8 SCAF14545, whole genome shotgun sequence | ||||||
![]() | HYDROLASE ACTIVATOR / Hydrolase / Zinc binding / carboxylation / Alpha-Beta Barrel | ||||||
Function / homology | ![]() pyrimidine nucleobase catabolic process / dihydropyrimidinase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsieh, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J. | ||||||
![]() | ![]() Title: Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function. Authors: Hsieh, Y.C. / Chen, M.C. / Hsu, C.C. / Chan, S.I. / Yang, Y.S. / Chen, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.3 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56930.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DPYS, GSTENG00015639001 / Plasmid: pET44a(+) / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-URP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE FIRST 20 RESIDUES ARE EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: lithium sulfate monohydrate (100mM), PEG4000 (12%, w/v), tris-sodium citrate dihydrate (100mM, pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2→30 Å / Num. all: 81631 / Num. obs: 81631 / % possible obs: 100 % / Observed criterion σ(F): 5.5 / Observed criterion σ(I): 5.5 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.518 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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