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Yorodumi- PDB-2b49: Crystal Structure of the Catalytic Domain of Protein Tyrosine Pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b49 | ||||||
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Title | Crystal Structure of the Catalytic Domain of Protein Tyrosine Phosphatase, non-receptor Type 3 | ||||||
Components | protein tyrosine phosphatase, non-receptor type 3 | ||||||
Keywords | HYDROLASE / Protein Tyrosine Phosphatase / non-receptor Type / Human / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase ...regulation of membrane depolarization during action potential / negative regulation of membrane protein ectodomain proteolysis / regulation of sodium ion transmembrane transporter activity / negative regulation of epidermal growth factor receptor signaling pathway / negative regulation of mitotic cell cycle / sodium channel regulator activity / cytoskeletal protein binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / liver regeneration / EGFR downregulation / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / MAPK cascade / ATPase binding / cytoskeleton / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Ugochukwu, E. / Arrowsmith, C. / Barr, A. / Bunkoczi, G. / Das, S. / Debreczeni, J. / Edwards, A. / Eswaran, J. / Knapp, S. / Sundstrom, M. ...Ugochukwu, E. / Arrowsmith, C. / Barr, A. / Bunkoczi, G. / Das, S. / Debreczeni, J. / Edwards, A. / Eswaran, J. / Knapp, S. / Sundstrom, M. / Turnbull, A. / von Delft, F. / Weigelt, J. / 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 | 2b49.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b49.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b49_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 2b49_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 2b49_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2b49_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b49 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b49 | HTTPS FTP |
-Related structure data
Related structure data | 2ahsC 2cfvC 2cjzC 2gjtC 2h4vC 2i75C 2jjdC 2nlkC 2nz6C 2oc3C 2ooqC 2p6xC 2pa5C 2qepC 3b7oC 1l8kS 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: 32747.457 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P26045, protein-tyrosine-phosphatase |
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#2: 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: 2.2 Å3/Da / Density % sol: 42.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Ammonium Sulphate, pH 5.5, 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: 1.008 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→43.39 Å / Num. obs: 41752 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.54→1.62 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L8K.pdb Resolution: 1.54→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.933 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.927 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 14.0445 Å / Origin y: 13.8071 Å / Origin z: 21.1315 Å
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