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- PDB-3wa5: Crystal Structure of type VI peptidoglycan muramidase effector Ts... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wa5 | ||||||
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Title | Crystal Structure of type VI peptidoglycan muramidase effector Tse3 in complex with its cognate immunity protein Tsi3 | ||||||
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![]() | HYDROLASE / PROTEIN-PROTEIN COMPLEX / muramidase | ||||||
Function / homology | ![]() host cell membrane / lysozyme / lysozyme activity / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ding, J. / Wang, T. / Liu, W. / Wang, D.C. | ||||||
![]() | ![]() Title: Complex structure of type VI peptidoglycan muramidase effector and a cognate immunity protein. Authors: Wang, T. / Ding, J. / Zhang, Y. / Wang, D.C. / Liu, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 100.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45741.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 16929.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% Jaffamine ED-2001, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.18 Å / Num. all: 41634 / Num. obs: 41634 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.4 % / Biso Wilson estimate: 14.59 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 28.8 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 11.8 / Num. unique all: 5971 / Rsym value: 0.335 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.942 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.01 Å2 / Biso mean: 14.39 Å2 / Biso min: 3.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.18 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: 15 / % reflection obs: 100 %
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