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- PDB-5m38: Structure of the TagL peptidoglycan binding domain from EAEC T6SS -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m38 | ||||||
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Title | Structure of the TagL peptidoglycan binding domain from EAEC T6SS | ||||||
![]() | OmpA family protein | ||||||
![]() | SUGAR BINDING PROTEIN / T6SS TagL Peptidoglycan binding domain | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cambillau, C. / Nguyen, V.S. / Spinelli, S. / Cascales, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the TagL peptidoglycan binding domain from EAEC T6SS Authors: Cambillau, C. / Nguyen, V.S. / Cascales, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.4 KB | Display | ![]() |
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PDB format | ![]() | 113.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3td5S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15093.977 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.36 Å3/Da / Density % sol: 71.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: mixing protein solution (5 mg/ml) with 0.1 M imidazole pH 6.5, 1.2 M NaAc PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.1 Å / Num. obs: 25065 / % possible obs: 99.8 % / Redundancy: 9 % / Biso Wilson estimate: 97.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.6→2.71 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.53 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TD5 Resolution: 2.6→45.1 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.199
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Displacement parameters | Biso mean: 85.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.434 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→45.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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