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- PDB-4hfl: Crystal structure of the type VI effector Tae4 from Enterobacter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hfl | ||||||
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Title | Crystal structure of the type VI effector Tae4 from Enterobacter cloacae | ||||||
![]() | Putative cytoplasmic protein | ||||||
![]() | HYDROLASE / amidase | ||||||
Function / homology | endopeptidase fold (from Nostoc punctiforme) - #70 / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta / Putative cytoplasmic protein / Putative cytoplasmic protein![]() | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
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PDB format | ![]() | 59.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.7 KB | Display | ![]() |
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Full document | ![]() | 417.7 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hffSC ![]() 4hfkC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19165.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.5M Ammonium sulfate, 0.1M Sodium citrate tribasic dehydrate pH5.6, 1.0M Lithium sulfate monohydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 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→50 Å / Num. all: 12215 / Num. obs: 12215 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 44.3 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 11.1 / Num. unique all: 593 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4HFF Resolution: 2.002→23.29 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.544 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.002→23.29 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 4.2922 Å / Origin y: -33.864 Å / Origin z: 3.2202 Å
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Refinement TLS group | Selection details: ALL |