[English] 日本語
![](img/lk-miru.gif)
- PDB-4lcq: The crystal structure of di-Zn dihydropyrimidinase in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4lcq | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of di-Zn dihydropyrimidinase in complex with NCBI | ||||||
![]() | dihydropyrimidinase | ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56930.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET44a(+) / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-URQ / ( | #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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.04 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: lithium sulfate monohydrate (100mM), PEG 4000 (12%, w/v), tris-sodium citrate dihydrate (100mM, pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||
Detector |
| ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. all: 110112 / Num. obs: 109892 / % possible obs: 99.8 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 4.4 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 25.341 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|