+Open data
-Basic information
Entry | Database: PDB / ID: 7ee3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PltC | ||||||
Components | Subtilase cytotoxin subunit B-like protein | ||||||
Keywords | TOXIN / Bacterial Toxin | ||||||
Function / homology | Enterotoxin / Subtilase cytotoxin subunit B-like protein Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Liu, X.Y. / Chen, Z. / Gao, X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Mbio / Year: 2022 Title: Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin. Authors: Liu, X. / Chen, Z. / Jiao, X. / Jiang, X. / Qiu, J. / You, F. / Long, H. / Cao, H. / Fowler, C.C. / Gao, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ee3.cif.gz | 267.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ee3.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ee3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ee3_validation.pdf.gz | 474.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ee3_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 7ee3_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 7ee3_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/7ee3 ftp://data.pdbj.org/pub/pdb/validation_reports/ee/7ee3 | HTTPS FTP |
-Related structure data
Related structure data | 7ee4C 7ee5C 7ee6C 5whtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13858.360 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A716TY65 #2: Chemical | ChemComp-PG4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.31 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 34% PEG500MME and 0.1M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→24.79 Å / Num. obs: 124886 / % possible obs: 98.35 % / Redundancy: 4.8 % / Biso Wilson estimate: 14.97 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.059 / Net I/σ(I): 32.45 |
Reflection shell | Resolution: 1.33→1.378 Å / Num. unique obs: 11420 / CC1/2: 0.938 / Rrim(I) all: 0.384 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WHT Resolution: 1.33→24.79 Å / SU ML: 0.1346 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.0517 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: 21.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→24.79 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|