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Yorodumi- PDB-4fge: Structure of the effector protein Tse1 from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fge | ||||||
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Title | Structure of the effector protein Tse1 from Pseudomonas aeruginosa | ||||||
Components | Tse1 | ||||||
Keywords | HYDROLASE / N1pC/P60 superfamily / peptidoglycan hydrolase / cytosol | ||||||
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: 1.7 Å | ||||||
Authors | Benz, J. / Sendlmeier, C. / Barends, T.R.M. / Meinhart, A. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structural Insights into the Effector - Immunity System Tse1/Tsi1 from Pseudomonas aeruginosa. Authors: Benz, J. / Sendlmeier, C. / Barends, T.R. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fge.cif.gz | 240.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fge.ent.gz | 195.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fge_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 4fge_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 4fge_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 4fge_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fge ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fge | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17743.064 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9I2Q1 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM KSCN, 1% (v/v) MPD, and 20% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9796 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 64182 / Num. obs: 63172 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.13 / Num. unique all: 9887 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.075 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.008 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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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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