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Open data
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Basic information
Entry | Database: PDB / ID: 1mhd | ||||||
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Title | CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA | ||||||
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![]() | COMPLEX (TRANSCRIPTION ACTIVATOR/DNA) / COMPLEX (TRANSCRIPTION ACTIVATOR-DNA) / SMAD3 MH1 / SMAD BINDING ELEMENT / ![]() | ||||||
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 | ![]() ![]() | ||||||
![]() | Shi, Y. | ||||||
![]() | ![]() Title: Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling. Authors: Shi, Y. / Wang, Y.F. / Jayaraman, L. / Yang, H. / Massague, J. / Pavletich, N.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.7 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | ![]() Mass: 3959.612 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | ![]() Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | ![]() Mass: 15539.169 Da / Num. of mol.: 2 / Fragment: MH1 DOMAIN, RESIDUES 1 - 144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 1998 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→20 Å / Num. obs: 9228 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.053 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 9 / Rsym value: 0.162 / % possible all: 96.5 |
Reflection | *PLUS Num. measured all: 39338 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.162 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.34 |