+Open data
-Basic information
Entry | Database: PDB / ID: 4q2n | ||||||
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Title | INADL PDZ3 in Complex with a Phage-Derived Peptide | ||||||
Components | InaD-like protein | ||||||
Keywords | PROTEIN BINDING / PDZ | ||||||
Function / homology | Function and homology information tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / centriolar satellite / bicellular tight junction / regulation of microtubule cytoskeleton organization ...tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / establishment of apical/basal cell polarity / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / centriolar satellite / bicellular tight junction / regulation of microtubule cytoskeleton organization / apical part of cell / cell junction / intracellular signal transduction / apical plasma membrane / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Appleton, B.A. / Wiesmann, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: A structural portrait of the PDZ domain family. Authors: Ernst, A. / Appleton, B.A. / Ivarsson, Y. / Zhang, Y. / Gfeller, D. / Wiesmann, C. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q2n.cif.gz | 240.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q2n.ent.gz | 194.6 KB | Display | PDB format |
PDBx/mmJSON format | 4q2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q2n_validation.pdf.gz | 488.4 KB | Display | wwPDB validaton report |
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Full document | 4q2n_full_validation.pdf.gz | 494.2 KB | Display | |
Data in XML | 4q2n_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4q2n_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/4q2n ftp://data.pdbj.org/pub/pdb/validation_reports/q2/4q2n | HTTPS FTP |
-Related structure data
Related structure data | 4q2oC 4q2pC 4q2qC 2iwnS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11064.448 Da / Num. of mol.: 6 / Fragment: unp residues 362-452 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INADL, PATJ / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NI35 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Sequence details | PHAGE-DERIVED PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER | |
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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: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.5 Details: 20% PEG monomethyl ether 5000, 0.1 M bis-tris (pH 6.5), VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→25 Å / Num. obs: 40881 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Χ2: 1.043 / Net I/σ(I): 17.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2iwn Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.823 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.04 Å2 / Biso mean: 36.154 Å2 / Biso min: 14.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.041 Å / Total num. of bins used: 25
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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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