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Yorodumi- PDB-7jzr: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jzr | |||||||||||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB | |||||||||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / PDZ domain / inhibitor / complex / peptidomimetic | |||||||||||||||
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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / 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 / apical protein localization / molecular sequestering activity / trans-Golgi network transport vesicle / 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) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | |||||||||||||||
Authors | Gill, N.P. / Madden, D.R. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published Title: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALAEB Authors: Gill, N.P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jzr.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzr.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 7jzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jzr_validation.pdf.gz | 858.9 KB | Display | wwPDB validaton report |
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Full document | 7jzr_full_validation.pdf.gz | 859.5 KB | Display | |
Data in XML | 7jzr_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7jzr_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzr ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzr | HTTPS FTP |
-Related structure data
Related structure data | 4nmoS S: Starting model for refinement |
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Similar structure data |
-Links
-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOPC, CAL, FIG / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HD26 #2: Protein/peptide | Mass: 1088.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5.5 mg/mL CAL PDZ, 1 mM LyCALAEB, 30% (w/v) PEG 8000, 100 mM NaCl, 100 mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.8263 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8263 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→42.72 Å / Num. obs: 23523 / % possible obs: 93.4 % / Redundancy: 8.66 % / Biso Wilson estimate: 18.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.075 / Net I/σ(I): 17.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NMO Resolution: 1.54→42.72 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 21.1 / Stereochemistry target values: ML
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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 max: 65.47 Å2 / Biso mean: 21.7966 Å2 / Biso min: 12.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→42.72 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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