[English] 日本語
Yorodumi- PDB-4f0v: Crystal structure of type effector Tse1 from Pseudomonas aeruginousa -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f0v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of type effector Tse1 from Pseudomonas aeruginousa | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | HYDROLASE / NlpC/P60 domain / type VI amidase effector | ||||||
Function / homology | Function and homology information gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Zhang, H. / Gao, Z.Q. / Dong, Y.H. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa. Authors: Zhang, H. / Gao, Z.Q. / Su, X.D. / Dong, Y.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4f0v.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4f0v.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f0v_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4f0v_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 4f0v_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4f0v_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/4f0v ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f0v | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20196.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2Q1 |
---|---|
#2: Chemical | ChemComp-SIN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Succinic acid pH 7.0, 15% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 23887 / Num. obs: 23887 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 67.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 11.3 / Num. unique all: 1164 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.6→32.522 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 15.03 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.238 Å2 / ksol: 0.386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→32.522 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -0.1357 Å / Origin y: -18.4117 Å / Origin z: 13.5131 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |