+
Open data
-
Basic information
Entry | Database: PDB / ID: 7wr0 | ||||||
---|---|---|---|---|---|---|---|
Title | P32 of caspase-4 C258A mutant | ||||||
![]() | Caspase-4 | ||||||
![]() | HYDROLASE / protease / mutant | ||||||
Function / homology | ![]() caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / NLRP3 inflammasome complex / CARD domain binding / caspase binding ...caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / NLRP3 inflammasome complex / CARD domain binding / caspase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / pyroptotic inflammatory response / protein autoprocessing / protein maturation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / lipopolysaccharide binding / NOD1/2 Signaling Pathway / positive regulation of inflammatory response / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / regulation of inflammatory response / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / lipid binding / apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hou, Y.J. / Zeng, H. / Shao, F. / Ding, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis. Authors: Hou, Y. / Zeng, H. / Li, Z. / Feng, N. / Meng, F. / Xu, Y. / Li, L. / Shao, F. / Ding, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wr1C ![]() 7wr2C ![]() 7wr3C ![]() 7wr4C ![]() 7wr5C ![]() 7wr6C ![]() 6kmtS 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: 32095.428 Da / Num. of mol.: 1 / Mutation: C258A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M potassium chloride |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.91 Å / Num. obs: 7706 / % possible obs: 99.5 % / Redundancy: 18.72 % / Biso Wilson estimate: 73.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.073 / Net I/σ(I): 35.98 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 3.66 / Num. unique obs: 551 / CC1/2: 0.882 / Rrim(I) all: 0.923 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6KMT Resolution: 2.8→36.16 Å / SU ML: 0.4717 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7611 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: 70.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→36.16 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|