+Open data
-Basic information
Entry | Database: PDB / ID: 3vpv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Pseudomonas aeruginosa Tsi2 | ||||||
Components | Tse2 specific immunity protein 2 | ||||||
Keywords | TOXIN INHIBITOR | ||||||
Function / homology | Helix Hairpins - #2500 / Tse2 immunity protein Tsi2 / : / T6SS, Immune protein Tsi2-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Immune protein Tsi2 Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Wang, W. / Ding, J. / Wang, D.C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Pseudomonas aeruginosa Tsi2 Authors: Wang, W. / Ding, J. / Wang, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vpv.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vpv.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vpv_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3vpv_full_validation.pdf.gz | 426.6 KB | Display | |
Data in XML | 3vpv_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3vpv_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/3vpv ftp://data.pdbj.org/pub/pdb/validation_reports/vp/3vpv | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9689.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2703 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9I0D9 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10% PEG 3350, 0.1mM sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9795 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.794 Å / Num. all: 12278 / Num. obs: 12200 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 16.878 Å2 / Rmerge(I) obs: 0.022 / Rsym value: 0.022 / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 16 / Num. unique all: 1771 / Rsym value: 0.047 / % possible all: 95.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.8→19.794 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8631 / SU ML: 0.21 / σ(F): 0.08 / Phase error: 21.31 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.089 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.61 Å2 / Biso mean: 16.23 Å2 / Biso min: 3.41 Å2
| ||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.794 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
|