[English] 日本語
Yorodumi- PDB-6jdp: the imm52 family protein TsiT (PA3908) from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jdp | ||||||
---|---|---|---|---|---|---|---|
Title | the imm52 family protein TsiT (PA3908) from Pseudomonas aeruginosa | ||||||
Components | Imm52 family protein | ||||||
Keywords | ANTITOXIN / Immunity protein / monomer / T6SS | ||||||
Function / homology | Imm52 family, TsiT-like / Immunity protein 52 / Immunity protein 52 / PHOSPHATE ION / Imm52 domain-containing protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å | ||||||
Authors | She, Z. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Protein Sci. / Year: 2019 Title: Structural characterization of the Imm52 family protein TsiT in Pseudomonas aeruginosa. Authors: She, Z. / Geng, Z. / Xu, J.H. / Li, Y.H. / Dong, Y.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jdp.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jdp.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/6jdp ftp://data.pdbj.org/pub/pdb/validation_reports/jd/6jdp | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29959.799 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA3908 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXA5 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.26 M Sodium phosphate monobasic monohydrate, 0.14 M Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 30138 / % possible obs: 100 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 19.417 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.222 / Num. unique obs: 1610 / CC1/2: 0.637 / Rsym value: 0.752 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.601→21.74 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.85
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.601→21.74 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|