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Yorodumi- PDB-7jzo: CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jzo | |||||||||||||||
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Title | CFTR Associated Ligand (CAL) PDZ domain bound to peptidomimetic LyCALTPP | |||||||||||||||
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: 1.61 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 LyCALTPP 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 | 7jzo.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jzo.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 7jzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jzo_validation.pdf.gz | 896.4 KB | Display | wwPDB validaton report |
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Full document | 7jzo_full_validation.pdf.gz | 896.8 KB | Display | |
Data in XML | 7jzo_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 7jzo_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/7jzo ftp://data.pdbj.org/pub/pdb/validation_reports/jz/7jzo | 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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1 |
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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: Chemical | #5: 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: 2.09 Å3/Da / Density % sol: 41.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 5.36 mg/mL CAL PDZ, 1 mM LyCALTPP, 31% (w/v) PEG 8000, 150 mM NaCl, 100 mM Tris pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792909 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792909 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.61→50 Å / Num. obs: 22749 / % possible obs: 98.4 % / Redundancy: 9.17 % / Biso Wilson estimate: 13.31 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.132 / Net I/σ(I): 15.84 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.61→48.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.02 / 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: 53.05 Å2 / Biso mean: 17.1044 Å2 / Biso min: 5.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→48.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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