[English] 日本語
Yorodumi- PDB-6ijf: Crystal structure of the type VI effector-immunity complex (Tae4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ijf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens | ||||||
Components |
| ||||||
Keywords | ANTITOXIN / COMPLEX | ||||||
Function / homology | Function and homology information endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular ...endopeptidase fold (from Nostoc punctiforme) - #80 / MYOD Basic-Helix-Loop-Helix Domain, subunit B - #80 / Rap1a immunity protein / Rap1a immunity proteins / Type VI secretion system (T6SS), amidase effector protein 4 / Type VI secretion system (T6SS), amidase effector protein 4 / MYOD Basic-Helix-Loop-Helix Domain, subunit B / endopeptidase fold (from Nostoc punctiforme) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex. Authors: Fukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ijf.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ijf.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ijf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/6ijf ftp://data.pdbj.org/pub/pdb/validation_reports/ij/6ijf | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ijeC 4bi8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.1453302 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
|
-Components
#1: Protein | Mass: 11482.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_4314 / Plasmid: modified pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID3 #2: Protein | Mass: 18120.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_4315 / Plasmid: modified pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID4 #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % / Mosaicity: 0 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 35 % PEG 400, 0.05 M Tris pH 8.5, 0.05 M sodium sulfate, 0.05 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 16, 2015 | ||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→97.18 Å / Num. obs: 44633 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Net I/σ(I): 15 / Num. measured all: 452487 / Scaling rejects: 117 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BI8 Resolution: 1.9→62.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.379 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.589 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→62.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|