+Open data
-Basic information
Entry | Database: PDB / ID: 2pa5 | ||||||
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Title | Crystal structure of human protein tyrosine phosphatase PTPN9 | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 9 | ||||||
Keywords | HYDROLASE / Protein tyrosine phosphatase / MEG2 / PTPN9 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information neuron projection terminus / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / positive regulation of protein localization to plasma membrane / negative regulation of neuron projection development / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ugochukwu, E. / Barr, A. / Pike, A.C.W. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A. / Uppenberg, J. / Bunkoczi, G. / Salah, E. / Das, S. ...Ugochukwu, E. / Barr, A. / Pike, A.C.W. / Savitsky, P. / Papagrigoriou, E. / Turnbull, A. / Uppenberg, J. / Bunkoczi, G. / Salah, E. / Das, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / 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 | 2pa5.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pa5.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pa5 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pa5 | HTTPS FTP |
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-Related structure data
Related structure data | 2ahsC 2b49C 2cfvC 2cjzC 2gjtC 2h4vC 2i75C 2jjdC 2nlkC 2nz6C 2oc3C 2ooqC 2p6xC 2qepC 3b7oC 2hnqS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 278 - 306 / Label seq-ID: 3 - 31
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-Components
#1: Protein | Mass: 36229.055 Da / Num. of mol.: 2 / Fragment: PTPN9: Tyrosine-protein phosphatase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN9 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) Strain (production host): Phage-resistant derivative of BL21(DE3) References: UniProt: P43378, protein-tyrosine-phosphatase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-SCN / | #4: Chemical | ChemComp-EDO / #5: 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: 1.99 Å3/Da / Density % sol: 38.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.15 Details: 25% PEG 3350, 0.2 M Potassium thiocyanate, 10% Ethylene glycol, 0.1 M Bis-Tris propane pH 6.15, 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: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.96 Å / Num. all: 71616 / Num. obs: 71616 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.1 / Num. unique all: 19981 / Rsym value: 0.379 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HNQ Resolution: 1.6→33.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.189 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→33.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.6→1.642 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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