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Open data
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Basic information
Entry | Database: PDB / ID: 1nte | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OF SYNTENIN | ||||||
![]() | Syntenin 1 | ||||||
![]() | SIGNALING PROTEIN / Syntenin / PDZ recognition | ||||||
Function / homology | ![]() interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / presynapse assembly / neurexin family protein binding / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / protein sequestering activity / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / ephrin receptor binding / adherens junction / positive regulation of JNK cascade / ionotropic glutamate receptor binding / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / Ras protein signal transduction / cytoskeleton / blood microparticle / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
![]() | ![]() Title: Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm. Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1obxC ![]() 1obyC ![]() 1obzC ![]() 1n99S S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 8709.964 Da / Num. of mol.: 1 / Fragment: PDZ 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-O / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.41 Å3/Da / Density % sol: 12.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→12.16 Å / Num. all: 18559 / Num. obs: 18559 / % possible obs: 73.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.5 |
Reflection | *PLUS Lowest resolution: 13 Å / Num. measured all: 58393 |
Reflection shell | *PLUS Highest resolution: 1.1 Å / Lowest resolution: 1.14 Å / % possible obs: 11 % / Num. unique obs: 275 / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.46 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1N99 Resolution: 1.24→12.16 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.603 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.045 / ESU R Free: 0.045 / 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: 10.391 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→12.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.272 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor Rfree: 0.153 / Rfactor Rwork: 0.113 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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