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Yorodumi- PDB-2z72: New Structure Of Cold-Active Protein Tyrosine Phosphatase At 1.1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z72 | ||||||
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Title | New Structure Of Cold-Active Protein Tyrosine Phosphatase At 1.1 Angstrom | ||||||
Components | Protein-tyrosine-phosphataseProtein tyrosine phosphatase | ||||||
Keywords | HYDROLASE / COLD-ACTIVE ENZYME / PSYCHROPHILE / PROTEIN TYROSINE PHOSPHATASE / SHEWANELLA SP. | ||||||
Function / homology | Function and homology information protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Shewanella sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å | ||||||
Authors | Tsuruta, H. / Mikami, B. / Yamamoto, C. / Yamagata, H. | ||||||
Citation | Journal: Febs J. / Year: 2008 Title: The role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphatase Authors: Tsuruta, H. / Mikami, B. / Yamamoto, C. / Yamagata, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z72.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z72.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z72 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z72 | HTTPS FTP |
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-Related structure data
Related structure data | 2zbmC 1v73S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38848.922 Da / Num. of mol.: 1 / Fragment: UNP residues 22-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella sp. (bacteria) / Gene: PPI / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S427, protein-tyrosine-phosphatase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THERE ARE CONFLICTS BETWEEN SEQRES(SER) AND SEQUENCE DATABASE (GLY). THE AUTHORS BELIEVE THAT THE ...THERE ARE CONFLICTS BETWEEN SEQRES(SER) AND SEQUENCE DATABASE (GLY). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% polyethyleneglycol, 0.1M ammonium acetate, 50mM p-nitrophenylsulphate, 0.05M Tris-HCl (pH8.5), pH8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 141407 / % possible obs: 89.2 % |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1V73 Resolution: 1.1→8 Å / Num. parameters: 32955 / Num. restraintsaints: 39804 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 39 / Occupancy sum hydrogen: 2670 / Occupancy sum non hydrogen: 3479.15 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→8 Å
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Refine LS restraints |
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