+Open data
-Basic information
Entry | Database: PDB / ID: 5z5b | ||||||
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Title | Crystal structure of Tk-PTP in the G95A mutant 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: 2.3 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 | 5z5b.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z5b.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z5b_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 5z5b_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 5z5b_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5z5b_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z5b ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z5b | HTTPS FTP |
-Related structure data
Related structure data | 5z59C 5z5aSC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18518.312 Da / Num. of mol.: 3 / Mutation: G95A 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: Chemical | |
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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: 3.13 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Bis-Tris (pH 6.25) and 0.8M magnesium formate dehydrate |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.298→77.4 Å / Num. obs: 28515 / % possible obs: 95.2 % / Redundancy: 4.3 % / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.298→2.34 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z5A Resolution: 2.3→77.4 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.346 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.243 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.539 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→77.4 Å
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Refine LS restraints |
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