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- PDB-4jof: CFTR Associated Ligand (CAL) PDZ domain bound to peptide L-iCAL36... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jof | ||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to peptide L-iCAL36 (ANSRLPTSII) | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / CFTR Associated Ligand / CAL / PIST / FIG | ||||||
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 / trans-Golgi network transport vesicle / molecular sequestering activity / 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 / trans-Golgi network transport vesicle / molecular sequestering activity / apical protein localization / RHOQ GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / transmembrane transporter binding / postsynaptic density / Golgi membrane / lysosomal membrane / dendrite / Golgi apparatus / protein-containing complex / identical protein binding / membrane / plasma membrane / cytoplasm 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 | ![]() | 89.6 KB | Display | ![]() |
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PDB format | ![]() | 68.3 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 ![]() 4jogC ![]() 4johC ![]() 4jojC ![]() 4jokC ![]() 4jopC ![]() 4jorC ![]() 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: 1072.237 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.95 Details: 36% (w/v) polyethylene glycol (PEG)8000, 0.2 M sodium chloride, 0.01 M tris(hydroxymethyl)aminomethane (Tris) hydrochloride (HCl), pH 7.95, 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 7, 2010 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→34.01 Å / Num. all: 53479 / Num. obs: 53402 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.24 / Rmerge(I) obs: 0.087 / Rsym value: 0.063 / Net I/σ(I): 20.98 | ||||||||||||||||||||||||||||||||||||||||||
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: 1.2→34.01 Å / SU ML: 0.14 / Cross valid method: Omit map / σ(F): 2 / Phase error: 17.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.85 Å2 / ksol: 0.445 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.2→34.01 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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