+Open data
-Basic information
Entry | Database: PDB / ID: 6d4f | ||||||
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Title | Crystal structure of PTP epsilon D2 domain (A455N/V457Y/E597D) | ||||||
Components | Receptor-type tyrosine-protein phosphatase epsilon | ||||||
Keywords | HYDROLASE / phosphatase | ||||||
Function / homology | Function and homology information transmembrane receptor protein tyrosine phosphatase activity / negative regulation of insulin receptor signaling pathway / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.909 Å | ||||||
Authors | Lountos, G.T. / Raran-Kurussi, S. / Zhao, B.M. / Dyas, B.K. / Austin, B.P. / Burke Jr., T.R. / Ulrich, R.G. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design. Authors: Lountos, G.T. / Raran-Kurussi, S. / Zhao, B.M. / Dyas, B.K. / Burke Jr., T.R. / Ulrich, R.G. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d4f.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d4f.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 6d4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d4f ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d4f | HTTPS FTP |
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-Related structure data
Related structure data | 6d3fC 6d4dC 2jjdS 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: 32426.822 Da / Num. of mol.: 1 / Fragment: epsilon D2 domain / Mutation: A455N, V457Y, E597D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRE / Plasmid: pSRK2612 / Production host: Escherichia coli (E. coli) / References: UniProt: P23469, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-1PE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.32 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M imidazole pH 8.0, 0.2 M calcium acetate hydrate, 20% (w/v) polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.909→50 Å / Num. obs: 26610 / % possible obs: 97.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.486 / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JJD Resolution: 1.909→40.015 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.909→40.015 Å
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Refine LS restraints |
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LS refinement shell |
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