[English] 日本語
![](img/lk-miru.gif)
- PDB-4hfk: Crystal structure of the type VI effector-immunity complex Tae4-T... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4hfk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the type VI effector-immunity complex Tae4-Tai4 from Enterobacter cloacae | ||||||
![]() |
| ||||||
![]() | HYDROLASE / amidase | ||||||
Function / homology | ![]() endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex ...endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, H. / Gao, Z.Q. / Dong, Y.H. | ||||||
![]() | ![]() Title: Structure of the type VI effector-immunity complex (Tae4-Tai4) provides novel insights into the inhibition mechanism of the effector by its immunity protein. Authors: Zhang, H. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / Liu, G.F. / Xu, J.H. / Su, X.D. / Dong, Y.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hffSC ![]() 4hflC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 19165.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11701.106 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.69 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium chloride, 0.1M Na/K phosphate pH 6.5, 25% (w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2012 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 36726 / Num. obs: 36726 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1834 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4HFF Resolution: 2.1→23.402 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 18.98 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.486 Å2 / ksol: 0.401 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→23.402 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %
|