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Yorodumi- PDB-1i7e: C-Terminal Domain Of Mouse Brain Tubby Protein bound to Phosphati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i7e | ||||||
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Title | C-Terminal Domain Of Mouse Brain Tubby Protein bound to Phosphatidylinositol 4,5-bis-phosphate | ||||||
Components | TUBBY PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / tubby filled-barrel beta-barrel filled-beta-roll 12-stranded-beta-barrel helix-filled-barrel obesity blindness deafness phosphoinositide phosphatidylinositol | ||||||
Function / homology | Function and homology information intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / photoreceptor cell maintenance / protein localization to cilium / response to stimulus / positive regulation of phagocytosis ...intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / photoreceptor cell maintenance / protein localization to cilium / response to stimulus / positive regulation of phagocytosis / G protein-coupled receptor binding / sensory perception of sound / cilium / retina development in camera-type eye / protein-containing complex binding / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Santagata, S. / Boggon, T.J. / Baird, C.L. / Shan, W.S. / Shapiro, L. | ||||||
Citation | Journal: Science / Year: 2001 Title: G-protein signaling through tubby proteins. Authors: Santagata, S. / Boggon, T.J. / Baird, C.L. / Gomez, C.A. / Zhao, J. / Shan, W.S. / Myszka, D.G. / Shapiro, L. #1: Journal: Science / Year: 1999 Title: Implication of Tubby Proteins as Transcription Factors by Structure-Based Functional Analysis Authors: Boggon, T.J. / Shan, W.S. / Santagata, S. / Myers, S.C. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i7e.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7e.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i7e_validation.pdf.gz | 717.1 KB | Display | wwPDB validaton report |
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Full document | 1i7e_full_validation.pdf.gz | 729.5 KB | Display | |
Data in XML | 1i7e_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1i7e_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7e ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7e | HTTPS FTP |
-Related structure data
Related structure data | 1c8zS 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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Unit cell |
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-Components
#1: Protein | Mass: 29997.193 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P50586 |
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#2: Chemical | ChemComp-IBS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% PEG 4000, 0.1M Hepes, 4% 2-propanol, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 21694 / Num. obs: 20653 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 6 / Num. unique all: 1845 / Rsym value: 0.241 / % possible all: 91.3 |
Reflection shell | *PLUS % possible obs: 91.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C8Z Resolution: 1.95→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1215636.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 101.1 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 4.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.301 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.333 |