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Yorodumi- PDB-2i75: Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i75 | ||||||
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Title | Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4) | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 4 | ||||||
Keywords | HYDROLASE / PTPN4 / PTP / tyrosine phosphatase / MEG-1 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane ...Toll Like Receptor 4 (TLR4) Cascade / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / glutamate receptor binding / MECP2 regulates neuronal receptors and channels / cytoskeletal protein binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / cytoskeleton / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Ugochukwu, E. / Barr, A. / Savitsky, P. / Burgess, N. / Das, S. / Turnbull, A. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. ...Ugochukwu, E. / Barr, A. / Savitsky, P. / Burgess, N. / Das, S. / Turnbull, A. / von Delft, F. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome. Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i75.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i75.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 2i75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i75_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 2i75_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 2i75_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2i75_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/2i75 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/2i75 | HTTPS FTP |
-Related structure data
Related structure data | 2ahsC 2b49SC 2cfvC 2cjzC 2gjtC 2h4vC 2jjdC 2nlkC 2nz6C 2oc3C 2ooqC 2p6xC 2pa5C 2qepC 3b7oC 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: 36681.641 Da / Num. of mol.: 1 / Fragment: PTPN4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)R3 / References: UniProt: P29074, protein-tyrosine-phosphatase | ||
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#2: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.1M HEPES, 0.1 M NaCl, 1.3 M (NH4)SO4. , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→38.92 Å / Num. all: 11901 / Num. obs: 11901 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.45→2.58 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B49 Resolution: 2.45→38.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 22.541 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.129 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.513 Å / Total num. of bins used: 20
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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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