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Yorodumi- PDB-6x1r: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x1r | ||||||
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Title | Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ2 (mbDLG-2) in spacegroup P212121 | ||||||
Components | mbDLG protein | ||||||
Keywords | SIGNALING PROTEIN / PDZ / protein-protein interaction / choanoflagellates / Monosiga brevicollis / peptide-binding domain | ||||||
Function / homology | Function and homology information receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / cell-cell adhesion / cell junction / plasma membrane Similarity search - Function | ||||||
Biological species | Monosiga brevicollis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Bamonte, H.A. / Amacher, J.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. Authors: Gao, M. / Mackley, I.G.P. / Mesbahi-Vasey, S. / Bamonte, H.A. / Struyvenberg, S.A. / Landolt, L. / Pederson, N.J. / Williams, L.I. / Bahl, C.D. / Brooks 3rd, L. / Amacher, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x1r.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x1r.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 6x1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/6x1r ftp://data.pdbj.org/pub/pdb/validation_reports/x1/6x1r | HTTPS FTP |
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-Related structure data
Related structure data | 6x1nC 6x1pC 6x1xC 6x20C 6x22C 6x23C 2bygS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 10847.223 Da / Num. of mol.: 1 / Fragment: second PDZ domain (UNP residues 93-192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 209 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9UT73 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate, pH 5, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2020 | ||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.3→40.3 Å / Num. obs: 28809 / % possible obs: 99.4 % / Redundancy: 6.04 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 1 / Rsym value: 0.033 / Net I/σ(I): 24.04 | ||||||||||||||||||
Reflection shell | CC1/2: 0.866 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2BYG Resolution: 1.3→40.299 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.66 / 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: 75.48 Å2 / Biso mean: 24.4252 Å2 / Biso min: 11.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→40.299 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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