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Open data
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Basic information
Entry | Database: PDB / ID: 5od6 | ||||||
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Title | Crystal structure of Smad3-MH1 bound to the GGCGC site. | ||||||
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Function / homology | ![]() nuclear mineralocorticoid receptor binding / negative regulation of lung blood pressure / regulation of miRNA transcription / positive regulation of transforming growth factor beta3 production / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaczmarska, Z. / Marquez, J.A. / Macias, M.J. | ||||||
![]() | ![]() Title: Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. Authors: Martin-Malpartida, P. / Batet, M. / Kaczmarska, Z. / Freier, R. / Gomes, T. / Aragon, E. / Zou, Y. / Wang, Q. / Xi, Q. / Ruiz, L. / Vea, A. / Marquez, J.A. / Massague, J. / Macias, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 120.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5meyC ![]() 5mezC ![]() 5mf0C ![]() 5nm9C ![]() 5odgC ![]() 1ozjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 15036.612 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GAMIVKRLLGWKKGEQNGQEEKWCEKAVKSLVKKLKKTGQLDELEKAITTQNVNTKCITIPRSLDGRLQVSHRKGLPHVIYCRLWRWPDLHSHHELRAMELCEFAFNMKKDEVCVNPYHYQRVETPVL Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 4900.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium acetate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→30 Å / Num. obs: 26771 / % possible obs: 99.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 48.92 Å2 / Net I/σ(I): 7.51 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1917 / Rrim(I) all: 1.119 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1ozj Resolution: 2→27.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso mean: 61.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→27.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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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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