+Open data
-Basic information
Entry | Database: PDB / ID: 7wr2 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryatal structure of OspC3 C-terminal ankyrin-repeat domain | ||||||
Components | OspC3 | ||||||
Keywords | TRANSFERASE / ADP-riboxanase / effector / ankyrin-repeat domain | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host signal transduction pathway / modulation by symbiont of defense-related host calcium ion flux / symbiont-mediated suppression of host calcium or calmodulin-mediated signal transduction / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / toxin activity / host cell cytoplasm / calmodulin binding / extracellular region Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Hou, Y.J. / Zeng, H. / Shao, F. / Ding, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wr2.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wr2.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/7wr2 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/7wr2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7wr0C 7wr1SC 7wr3C 7wr4C 7wr5C 7wr6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18366.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: R4X5L7 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 28.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG monomethyl ether 550, 0.1 M Bis-Tris propane pH 9.0 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→40.1 Å / Num. obs: 19087 / % possible obs: 98.6 % / Redundancy: 6.02 % / Biso Wilson estimate: 17.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.049 / Net I/σ(I): 22.58 |
Reflection shell | Resolution: 1.54→1.58 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 7.87 / Num. unique obs: 1304 / CC1/2: 0.977 / Rrim(I) all: 0.176 / % possible all: 92.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WR1 Resolution: 1.54→40.09 Å / SU ML: 0.1318 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 18.0133 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: 21.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→40.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|