+
Open data
-
Basic information
Entry | Database: PDB / ID: 7x4f | ||||||
---|---|---|---|---|---|---|---|
Title | Native CD-NTase LpCdnE | ||||||
![]() | Cyclic dipyrimidine nucleotide synthase | ||||||
![]() | TRANSFERASE / CD-NTase / cGAS / cyclic dinucleotide | ||||||
Function / homology | ![]() nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y. / Ko, T.P. / Yang, C.S. / Wang, Y.C. / Hou, M.H. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases. Authors: Yang, C.S. / Ko, T.P. / Chen, C.J. / Hou, M.H. / Wang, Y.C. / Chen, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 163.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 438.6 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x4aSC ![]() 7x4cC ![]() 7x4gC ![]() 7x4pC ![]() 7x4qC ![]() 7x4tC ![]() 8hykC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34961.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DSP3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.55 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MgCl2, Tris, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 14892 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.54 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.047 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1507 / CC1/2: 0.652 / Rpim(I) all: 0.378 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7X4A Resolution: 2.46→28.97 Å / SU ML: 0.2436 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.8948 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→28.97 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|