[English] 日本語
![](img/lk-miru.gif)
- PDB-7mw8: Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7mw8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase | ||||||
![]() |
| ||||||
![]() | HYDROLASE / enzyme / nucleotide / pyrophosphatase / phosphodiesterase / bacterial | ||||||
Function / homology | Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / transferase activity / hydrolase activity / RNA / Alkaline phosphatase family protein![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Fernandez, D. / Li, L. / Brown, J.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: ENPP1's regulation of extracellular cGAMP is a ubiquitous mechanism of attenuating STING signaling. Authors: Carozza, J.A. / Cordova, A.F. / Brown, J.A. / AlSaif, Y. / Bohnert, V. / Cao, X. / Mardjuki, R.E. / Skariah, G. / Fernandez, D. / Li, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 457.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 368 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 549.8 KB | Display | |
Data in XML | ![]() | 81.5 KB | Display | |
Data in CIF | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n1sC ![]() 2gsuS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45993.855 Da / Num. of mol.: 6 / Mutation: T90A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | Mass: 629.454 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017 Details: Rh coated collimating mirrors, K-B focusing mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→121.042 Å / Num. all: 155855 / Num. obs: 155855 / % possible obs: 95 % / Redundancy: 2.9 % / Rpim(I) all: 0.089 / Rrim(I) all: 0.16 / Rsym value: 0.132 / Net I/av σ(I): 2.1 / Net I/σ(I): 3.7 / Num. measured all: 449161 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2GSU Resolution: 1.9→30.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.479 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 97.72 Å2 / Biso mean: 37.325 Å2 / Biso min: 15.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→30.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|