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Yorodumi- PDB-4r0t: Crystal structure of P. aeruginosa TpbA (C132S) in complex with pTyr -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r0t | ||||||
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Title | Crystal structure of P. aeruginosa TpbA (C132S) in complex with pTyr | ||||||
Components | Protein tyrosine phosphatase TpbA | ||||||
Keywords | HYDROLASE / DUSP fold / protein tyrosine phosphatase | ||||||
Function / homology | Function and homology information protein-serine/threonine phosphatase / phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å | ||||||
Authors | Xu, K. / Li, S. / Wang, Y. / Bartlam, M. | ||||||
Citation | Journal: Plos One Title: Structural and Biochemical Analysis of Tyrosine Phosphatase Related to Biofilm Formation A (TpbA) from the Opportunistic Pathogen Pseudomonas aeruginosa PAO1 Authors: Xu, K. / Li, S. / Yang, W. / Li, K. / Bai, Y. / Xu, Y. / Jin, J. / Wang, Y. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r0t.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r0t.ent.gz | 113 KB | Display | PDB format |
PDBx/mmJSON format | 4r0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r0t ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r0t | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23991.398 Da / Num. of mol.: 2 / Mutation: C132S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tpbA, PA3885 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXC7 #2: Chemical | ChemComp-TYR / | #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15%(w/v) PEG10000, 0.1M citrate, 2%(v/v) dioxane, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2014 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 11739 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→28.517 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 28.48 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 193.15 Å2 / Biso mean: 64.7115 Å2 / Biso min: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→28.517 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: 8
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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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