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Yorodumi- PDB-3vpj: crystal structure of type VI effector Tse1 from Pseudomonas aerug... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vpj | ||||||
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Title | crystal structure of type VI effector Tse1 from Pseudomonas aeruginosa in complex with immune protein Tsi1 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information gamma-D-glutamyl-meso-diaminopimelate peptidase / amidase activity / host cell membrane / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ding, J. / Wang, W. / Wang, D.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural insights into the Pseudomonas aeruginosa type VI virulence effector Tse1 bacteriolysis and self-protection mechanisms Authors: Ding, J. / Wang, W. / Feng, H. / Zhang, Y. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vpj.cif.gz | 234 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vpj.ent.gz | 195.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vpj_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
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Full document | 3vpj_full_validation.pdf.gz | 504.9 KB | Display | |
Data in XML | 3vpj_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 3vpj_validation.cif.gz | 63.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/3vpj ftp://data.pdbj.org/pub/pdb/validation_reports/vp/3vpj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18630.045 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1844 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q1 #2: Protein | Mass: 20949.334 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1845 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I2Q0 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 20% PEG 4000, 20% isopropanol, 0.1M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→63.61 Å / Num. all: 56237 / Num. obs: 56166 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.6 / Num. unique all: 8041 / Rsym value: 0.387 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.97 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8012 / SU ML: 0.37 / σ(F): 0 / Phase error: 26.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.518 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.58 Å2 / Biso mean: 52.87 Å2 / Biso min: 18.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.97 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: 20
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