[English] 日本語
![](img/lk-miru.gif)
- PDB-5z7c: crystal structure of cyclic GMP-AMP specifc phosphodiesterases in... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5z7c | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of cyclic GMP-AMP specifc phosphodiesterases in V.cholerae (V-cGAP3) | ||||||
![]() | 3'3'-cGAMP-specific phosphodiesterase 3 | ||||||
![]() | METAL BINDING PROTEIN / Cyclic dinucleotides / phosphodiesterase. | ||||||
Function / homology | ![]() cyclic-nucleotide phosphodiesterase activity / cyclic nucleotide catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, M.J. / Ye, Z.Y. / Su, X.D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3. Authors: Deng, M.J. / Tao, J. / E, C. / Ye, Z.Y. / Jiang, Z. / Yu, J. / Su, X.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 145.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 51564.652 Da / Num. of mol.: 1 / Mutation: K440A/K441A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: VC_A0931 Production host: ![]() References: UniProt: Q9KL18, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.75 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 3350, 0.2M ammonium citrate tribasic, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→50 Å / Num. obs: 26853 / % possible obs: 99.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.85 |
Reflection shell | Resolution: 2.76→2.9 Å / Rmerge(I) obs: 0.898 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→28.595 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 53.9313 Å / Origin y: 49.4692 Å / Origin z: 107.9062 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |