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- PDB-2oc3: Crystal Structure of the Catalytic Domain of Human Protein Tyrosi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oc3 | ||||||
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Title | Crystal Structure of the Catalytic Domain of Human Protein Tyrosine Phosphatase non-receptor Type 18 | ||||||
![]() | Tyrosine-protein phosphatase non-receptor type 18 | ||||||
![]() | HYDROLASE / Protein Tyrosine Phosphatase / Receptor / Human / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() negative regulation of ERBB signaling pathway / blastocyst formation / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus ...negative regulation of ERBB signaling pathway / blastocyst formation / Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / Downregulation of ERBB2 signaling / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ugochukwu, E. / Barr, A. / Alfano, I. / Gorrec, F. / Umeano, C. / Savitsky, P. / Sobott, F. / Eswaran, J. / Papagrigoriou, E. / Debreczeni, J.E. ...Ugochukwu, E. / Barr, A. / Alfano, I. / Gorrec, F. / Umeano, C. / Savitsky, P. / Sobott, F. / Eswaran, J. / Papagrigoriou, E. / Debreczeni, J.E. / Turnbull, A. / Bunkoczi, G. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ahsC ![]() 2b49SC ![]() 2cfvC ![]() 2cjzC ![]() 2gjtC ![]() 2h4vC ![]() 2i75C ![]() 2jjdC ![]() 2nlkC ![]() 2nz6C ![]() 2ooqC ![]() 2p6xC ![]() 2pa5C ![]() 2qepC ![]() 3b7oC ![]() 1gwzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34296.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.24 % |
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Crystal grow | Temperature: 277 K / pH: 6.8 Details: 0.1M HEPES, 25% PEG-3350, 6% Jeffamine M-600, pH 6.8, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97875 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.24 Å / Num. obs: 44277 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3.4 / Num. unique all: 19366 / Rsym value: 0.343 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entries 2B49, 1GWZ Resolution: 1.5→38.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.069 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / 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: 11.822 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→38.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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