+Open data
-Basic information
Entry | Database: PDB / ID: 5z5a | ||||||
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Title | Crystal structure of Tk-PTP in the active form | ||||||
Components | Protein-tyrosine phosphatase | ||||||
Keywords | HYDROLASE / tyrosine phosphatase | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis KOD1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ku, B. / Yun, H.Y. / Kim, S.J. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1 Authors: Yun, H.Y. / Lee, J. / Kim, H. / Ryu, H. / Shin, H.C. / Oh, B.H. / Ku, B. / Kim, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z5a.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z5a.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 5z5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z5a ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z5a | HTTPS FTP |
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-Related structure data
Related structure data | 5z59SC 5z5bC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17172.756 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea) Strain: KOD1 / Gene: Tk-ptp, TK0241 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X270 #2: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.03M citric acid, 0.07M Bis-Tris propane (pH 7.6), 8%(w/v) polyethylene glycol 3350, 0.08M spermine tetrahydrochloride |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→50 Å / Num. obs: 45504 / % possible obs: 97.6 % / Redundancy: 4.7 % / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.8→1.83 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z59 Resolution: 1.8→27.96 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 19.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.96 Å
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Refine LS restraints |
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LS refinement shell |
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