[English] 日本語
Yorodumi- PDB-7bba: Structure of the TagL peptidoglycan binding domain from EAEC T6SS -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bba | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the TagL peptidoglycan binding domain from EAEC T6SS | |||||||||
Components | Putative type VI secretion protein | |||||||||
Keywords | PROTEIN BINDING / Peptidoglycan binding protein / type VI secretion system | |||||||||
Function / homology | Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / membrane / Type VI secretion protein Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | |||||||||
Authors | Nguyen, V.S. / Cambillau, C. / Leone, P. | |||||||||
Funding support | France, 1items
| |||||||||
Citation | Journal: Plos One / Year: 2021 Title: Anchoring the T6SS to the cell wall: Crystal structure of the peptidoglycan binding domain of the TagL accessory protein. Authors: Nguyen, V.S. / Spinelli, S. / Cascales, E. / Roussel, A. / Cambillau, C. / Leone, P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bba.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bba.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 7bba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bba_validation.pdf.gz | 350.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7bba_full_validation.pdf.gz | 355.4 KB | Display | |
Data in XML | 7bba_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 7bba_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bba ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bba | HTTPS FTP |
-Related structure data
Related structure data | 5m38S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15130.050 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EC042_4528 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 / References: UniProt: D3GUV9 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 5.5-6.5 0.6-1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.919762 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919762 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→34.9 Å / Num. obs: 21834 / % possible obs: 99.7 % / Redundancy: 21.1 % / Biso Wilson estimate: 72.08 Å2 / CC1/2: 0.991 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.43→2.57 Å / Num. unique obs: 3454 / CC1/2: 0.777 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M38 Resolution: 2.43→34.9 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.419 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.413 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.246
| ||||||||||||||||||||||||
Displacement parameters | Biso max: 122.73 Å2 / Biso mean: 75.57 Å2 / Biso min: 30 Å2
| ||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→34.9 Å
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.43→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
|