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Yorodumi- PDB-3o4t: Crystal Structure of HePTP with an Open WPD Loop and Partially De... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o4t | ||||||
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Title | Crystal Structure of HePTP with an Open WPD Loop and Partially Depleted Active Site | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 7 | ||||||
Keywords | HYDROLASE / HEPTP / HUMAN HEMATOPOIETIC TYROSINE PHOSPHATASE CATALYTIC DOMAIN MUTANT / LC-PTP / PTPN7 | ||||||
Function / homology | Function and homology information Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitotic spindle / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade ...Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / mitotic spindle / cytoplasmic side of plasma membrane / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Critton, D.A. / Page, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Visualizing active-site dynamics in single crystals of HePTP: opening of the WPD loop involves coordinated movement of the E loop. Authors: Critton, D.A. / Tautz, L. / Page, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o4t.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o4t.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o4t_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
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Full document | 3o4t_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 3o4t_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3o4t_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4t ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4t | HTTPS FTP |
-Related structure data
Related structure data | 3o4sSC 3o4uC 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: 35232.801 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 65-360 / Mutation: S72D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P35236, protein-tyrosine-phosphatase | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-TAR / | ||
#4: Chemical | #5: 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: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 17, 2009 / Details: RIGAKU OSMIC CONFOCAL OPTIC |
Radiation | Monochromator: RIGAKU OSMIC CONFOCAL OPTIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 9939 / Num. obs: 8972 / % possible obs: 90.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 385 / Rsym value: 0.296 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3O4S Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.567 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES AND SIDECHAINS FOR WHICH NO DENSITY WAS OBSERVED WERE NOT MODELED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.955 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.663 Å / Total num. of bins used: 20
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