+Open data
-Basic information
Entry | Database: PDB / ID: 2ooq | ||||||
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Title | Crystal Structure of the Human Receptor Phosphatase PTPRT | ||||||
Components | Receptor-type tyrosine-protein phosphatase T | ||||||
Keywords | HYDROLASE / Protein Tyrosine Phosphatase / receptor / Human / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / delta-catenin binding / alpha-catenin binding / cellular response to interleukin-6 / negative regulation of receptor signaling pathway via STAT / STAT family protein binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules ...gamma-catenin binding / transmembrane receptor protein tyrosine phosphatase activity / delta-catenin binding / alpha-catenin binding / cellular response to interleukin-6 / negative regulation of receptor signaling pathway via STAT / STAT family protein binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / peptidyl-tyrosine dephosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / protein dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / beta-catenin binding / protein phosphatase binding / membrane => GO:0016020 / cell adhesion / cadherin binding / cell surface / signal transduction / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ugochukwu, E. / Alfano, I. / Barr, A. / Keates, T. / Eswaran, J. / Salah, E. / Savitsky, P. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C.H. ...Ugochukwu, E. / Alfano, I. / Barr, A. / Keates, T. / Eswaran, J. / Salah, E. / Savitsky, P. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / 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 | 2ooq.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ooq.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ooq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ooq_validation.pdf.gz | 946.1 KB | Display | wwPDB validaton report |
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Full document | 2ooq_full_validation.pdf.gz | 952.5 KB | Display | |
Data in XML | 2ooq_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 2ooq_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/2ooq ftp://data.pdbj.org/pub/pdb/validation_reports/oo/2ooq | HTTPS FTP |
-Related structure data
Related structure data | 2ahsC 2b49C 2cfvC 2cjzC 2gjtC 2h4vC 2i75C 2jjdC 2nlkC 2nz6C 2oc3C 2p6xC 2pa5C 2qepC 3b7oC 1larS 1rpmS 2c7sS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 32763.082 Da / Num. of mol.: 2 / Fragment: PTPRT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRT, KIAA0283 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: O14522, protein-tyrosine-phosphatase #2: Chemical | #3: Chemical | ChemComp-NA / | #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: 2.21 Å3/Da / Density % sol: 44.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M LiCl, 0.1M HEPES, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→89.77 Å / Num. obs: 52802 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.595 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1RPM, 2C7S, 1LAR, 2FH7 Resolution: 1.8→89.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.669 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / 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: 22.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→89.77 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: 1.8→1.85 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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