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Yorodumi- PDB-2h4v: Crystal Structure of the Human Tyrosine Receptor Phosphatase Gamma -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h4v | ||||||
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Title | Crystal Structure of the Human Tyrosine Receptor Phosphatase Gamma | ||||||
Components | Receptor-type tyrosine-protein phosphatase gamma | ||||||
Keywords | HYDROLASE / TYROSINE RECEPTOR PHOSPHATASE / GAMMA / HUMAN / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information negative regulation of epithelial cell migration / transmembrane receptor protein tyrosine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of neuron projection development / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ugochukwu, E. / Barr, A. / Das, S. / Eswaran, J. / Savitsky, P. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Debreczeni, J. ...Ugochukwu, E. / Barr, A. / Das, S. / Eswaran, J. / Savitsky, P. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Debreczeni, J. / von Delft, F. / 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 | 2h4v.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h4v.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/2h4v ftp://data.pdbj.org/pub/pdb/validation_reports/h4/2h4v | HTTPS FTP |
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-Related structure data
Related structure data | 2ahsC 2b49C 2cfvC 2cjzC 2gjtC 2i75C 2jjdC 2nlkC 2nz6C 2oc3C 2ooqC 2p6xC 2pa5C 2qepC 3b7oC 2fh7S 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37112.023 Da / Num. of mol.: 2 / Fragment: PTPRG (residues 831-1127) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRG / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-R3 / References: UniProt: P23470, protein-tyrosine-phosphatase |
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-Non-polymers , 6 types, 575 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-FLC / | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-NA / | #7: 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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Ammonium acetate, citrate, PEG4K, pH 5.6, 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: 0.97925 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.23 Å / Num. obs: 105096 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.55→1.63 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FH7 Resolution: 1.55→47.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.443 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / 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: 16.125 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→47.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 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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