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Open data
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Basic information
Entry | Database: PDB / ID: 7pee | |||||||||
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Title | Crystal structure of extracellular part of human Trop2 | |||||||||
![]() | Tumor-associated calcium signal transducer 2 | |||||||||
![]() | MEMBRANE PROTEIN / extracellular part / dimer | |||||||||
Function / homology | ![]() negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / negative regulation of cell motility / regulation of epithelial cell proliferation / response to stimulus / negative regulation of stress fiber assembly ...negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / negative regulation of cell motility / regulation of epithelial cell proliferation / response to stimulus / negative regulation of stress fiber assembly / lateral plasma membrane / visual perception / basal plasma membrane / extracellular space / extracellular exosome / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pavsic, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM. Authors: Pavsic, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.2 KB | Display | ![]() |
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PDB format | ![]() | 159.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mzvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28381.301 Da / Num. of mol.: 4 / Mutation: N120Q,N208Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.05 Å3/Da / Density % sol: 75.63 % / Description: rod |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 1.6 M ammonium sulfate, 0.5 M NaCl, 0.0133 M EDTA, 0.1 M MES pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→48.38 Å / Num. obs: 57322 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.21 Å2 / CC1/2: 0.998 / Rsym value: 0.1157 / Net I/σ(I): 15.14 |
Reflection shell | Resolution: 2.81→2.98 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 9084 / CC1/2: 0.717 / Rsym value: 1.19 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MZV Resolution: 2.81→48.37 Å / SU ML: 0.4202 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8396 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→48.37 Å
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Refine LS restraints |
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LS refinement shell |
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