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- PDB-4h00: The crystal structure of mon-Zn dihydropyrimidinase from Tetraodo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h00 | ||||||
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Title | The crystal structure of mon-Zn dihydropyrimidinase from Tetraodon nigroviridis | ||||||
![]() | dihydropyrimidinase | ||||||
![]() | HYDROLASE / carboxylation / zinc binding / 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: Lysine Carboxylation: Metal and Structural Requirements for Post-translational Modification 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 | ![]() | 107.9 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 21.7 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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 / Plasmid: pET44a(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: lithium sulfate monohydrate, PEG 4000 (12%, w/v), tris-sodium citrate dihydrate (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 |
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Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 40712 / Num. obs: 40386 / % possible obs: 99.2 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.042 | |||||||||||||||
Reflection shell | Resolution: 2→2.03 Å / % possible all: 99.6 |
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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: 28.872 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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