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Yorodumi- PDB-4k78: CFTR Associated Ligand (CAL) E317A PDZ domain bound to peptide iC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k78 | ||||||
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Title | CFTR Associated Ligand (CAL) E317A PDZ domain bound to peptide iCAL36-QDTRL (ANSRWQDTRL) | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / CAL / PIST / FIG / PDZ-peptide complex / CFTR Associated Ligand / CFTR / PEPTIDE BINDING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Amacher, J.F. / Madden, D.R. | ||||||
Citation | Journal: Structure / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k78.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k78.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 4k78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k78_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 4k78_full_validation.pdf.gz | 431.4 KB | Display | |
Data in XML | 4k78_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 4k78_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k78 ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k78 | HTTPS FTP |
-Related structure data
Related structure data | 4joeC 4jofC 4jogC 4johC 4jojC 4jokC 4jopC 4jorC 4k6yC 4k72C 4k75C 4k76C 4e34S C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9375.748 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: E317A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HD26 |
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#2: Protein/peptide | Mass: 1248.349 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: 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: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40% (w/v) polyethylene glycol (PEG), 0.9 M sodium thiosulfate pentahydrate, 0.1 M tris(hydroxymethyl)aminomethane (Tris), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2013 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: S1 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→19.133 Å / Num. all: 10797 / Num. obs: 10781 / % possible obs: 99.9 % / Observed criterion σ(F): 2.04 / Observed criterion σ(I): 6.53 / Rsym value: 0.11 / Net I/σ(I): 26.01 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4E34 (CAL PDZ bound to iCAL36 peptide) Resolution: 1.8→19.133 Å / SU ML: 0.19 / Cross valid method: Omit map / σ(F): 2.04 / σ(I): 6.53 / Phase error: 17.02 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.834 Å2 / ksol: 0.497 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.133 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.5397 Å / Origin y: 23.4476 Å / Origin z: 36.7985 Å
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Refinement TLS group | Selection details: CHAIN A AND RESID 284:370 |