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- PDB-5nm9: Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nm9 | ||||||
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Title | Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site. | ||||||
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![]() | TRANSCRIPTION / Smads / transcription factor / DNA complex | ||||||
Function / homology | ![]() heteromeric SMAD protein complex / SMAD protein signal transduction / I-SMAD binding / anatomical structure morphogenesis / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaczmarska, Z. / Freier, R. / 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 | ![]() | 152.8 KB | Display | ![]() |
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PDB format | ![]() | 118.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5meySC ![]() 5mezC ![]() 5mf0C ![]() 5od6C ![]() 5odgC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15985.443 Da / Num. of mol.: 2 / Fragment: MH1 domain, UNP residues 33-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 5518.555 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: 2.41 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 4.8% PEG 4000, 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 77.62 Å2 |
Reflection shell | Resolution: 2.43→2.44 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 204 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MEY Resolution: 2.43→29.46 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.39 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.246
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Displacement parameters | Biso mean: 82.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.43→29.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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