[English] 日本語
Yorodumi- PDB-3wa5: Crystal Structure of type VI peptidoglycan muramidase effector Ts... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wa5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of type VI peptidoglycan muramidase effector Tse3 in complex with its cognate immunity protein Tsi3 | ||||||
Components |
| ||||||
Keywords | HYDROLASE / PROTEIN-PROTEIN COMPLEX / muramidase | ||||||
Function / homology | Function and homology information host cell membrane / lysozyme / lysozyme activity / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Ding, J. / Wang, T. / Liu, W. / Wang, D.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wa5.cif.gz | 124 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wa5.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wa5 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wa5 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 45741.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3484 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYC5 | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 16929.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3485 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYC4 | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.97 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.9→49.18 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8827 / SU ML: 0.19 / σ(F): 0 / Phase error: 18.26 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→49.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %
|