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Yorodumi- PDB-8bp4: Crystal structure of Trichoplax Scribble PDZ2 domain in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bp4 | |||||||||
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Title | Crystal structure of Trichoplax Scribble PDZ2 domain in complex with Trichoplax Vangl peptide | |||||||||
Components |
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Keywords | PROTEIN BINDING / PDZ domain / cell polarity / Scribble / Vangl / Trichoplax | |||||||||
Function / homology | Function and homology information neurotransmitter receptor transport postsynaptic membrane to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / adherens junction / cell-cell adhesion / basolateral plasma membrane / postsynaptic membrane / postsynaptic density / cytoplasm Similarity search - Function | |||||||||
Biological species | Trichoplax sp. H2 (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Maddumage, J.C. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To be published Title: Crystal structure of Trichoplax Scribble PDZ2 domain in complex with Trichoplax Vangl peptide Authors: Maddumage, J.C. / Humbert, P.O. / Kvansakul, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bp4.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bp4.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 8bp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bp4 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bp4 | HTTPS FTP |
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-Related structure data
Related structure data | 7jo7S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 9890.254 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_005790 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): codon + / References: UniProt: A0A369S7Y8 #2: Protein/peptide | Mass: 856.877 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata) #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.16 Å3/Da / Density % sol: 42.96 % / Description: Cubes |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulphate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→43.39 Å / Num. obs: 91308 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.15→1.17 Å / Rmerge(I) obs: 1.328 / Num. unique obs: 4253 / CC1/2: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JO7 Resolution: 1.15→42.3 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5445 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 27.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→42.3 Å
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Refine LS restraints |
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LS refinement shell |
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