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- PDB-4jor: CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncopro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jor | ||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to HPV18 E6 oncoprotein C-terminal peptide (RLQRRRETQV) | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / ![]() ![]() | ||||||
Function / homology | ![]() negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport ...negative regulation of anion channel activity / RHO GTPases regulate CFTR trafficking / negative regulation of protein localization to cell surface / Golgi-associated vesicle membrane / Golgi to plasma membrane transport / molecular sequestering activity / trans-Golgi network transport vesicle / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amacher, J.F. / Madden, D.R. | ||||||
![]() | ![]() Title: Stereochemical Preferences Modulate Affinity and Selectivity among Five PDZ Domains that Bind CFTR: Comparative Structural and Sequence Analyses. Authors: Amacher, J.F. / Cushing, P.R. / Brooks, L. / Boisguerin, P. / Madden, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.5 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4joeC ![]() 4jofC ![]() 4jogC ![]() 4johC ![]() 4jojC ![]() 4jokC ![]() 4jopC ![]() 4k6yC ![]() 4k72C ![]() 4k75C ![]() 4k76C ![]() 4k78C ![]() 4e34S C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9353.722 Da / Num. of mol.: 2 / Fragment: CAL PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1345.554 Da / Num. of mol.: 2 / Fragment: HPV18 E6 peptide / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.06 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 29% (w/v) polyethylene glycol (PEG), 0.075 M sodium chloride, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2012 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.34→19.29 Å / Num. all: 36592 / Num. obs: 34483 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 7.53 / Rmerge(I) obs: 0.05 / Rsym value: 0.038 / Net I/σ(I): 36.69 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4E34 (CAL PDZ domain bound to iCAL36 peptide) Resolution: 1.34→19.29 Å / SU ML: 0.16 / Cross valid method: Omit map / σ(F): 2 / σ(I): 7.53 / Phase error: 17.36 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.62 Å2 / ksol: 0.45 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.34→19.29 Å
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Refine LS restraints |
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LS refinement shell |
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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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