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- PDB-5x6m: Crystal Structure of SMAD5-MH1 in complex with a composite DNA se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x6m | |||||||||
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Title | Crystal Structure of SMAD5-MH1 in complex with a composite DNA sequence | |||||||||
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![]() | METAL BINDING PROTEIN/DNA / Smad5 MH1 domain / composite DNA / SBE DNA / GC-rich DNA / METAL BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() negative regulation of Fas signaling pathway / Mullerian duct regression / Signaling by BMP / osteoblast fate commitment / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development ...negative regulation of Fas signaling pathway / Mullerian duct regression / Signaling by BMP / osteoblast fate commitment / heteromeric SMAD protein complex / DEAD/H-box RNA helicase binding / embryonic pattern specification / SMAD protein signal transduction / I-SMAD binding / cartilage development / ureteric bud development / germ cell development / cellular response to organic cyclic compound / anatomical structure morphogenesis / BMP signaling pathway / positive regulation of osteoblast differentiation / cardiac muscle contraction / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / bone development / DNA-binding transcription repressor activity, RNA polymerase II-specific / angiogenesis / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chai, N. / Wang, J. / Wang, Z.X. / Wu, J.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the Smad5 MH1 domain to recognize different DNA sequences. Authors: Chai, N. / Li, W.X. / Wang, J. / Wang, Z.X. / Yang, S.M. / Wu, J.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.1 KB | Display | ![]() |
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PDB format | ![]() | 238.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.2 KB | Display | ![]() |
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Full document | ![]() | 487.1 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x6gC ![]() 5x6hC ![]() 3kmpS 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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Unit cell |
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Components
#1: Protein | Mass: 17322.232 Da / Num. of mol.: 4 / Fragment: MH1 domain (UNP RESIDUES 1-143) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 6736.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 6767.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-tris, pH 6.5, 0.2M LiNO3, 8% PEG 3350, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2014 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979065 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→40 Å / Num. obs: 24244 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.046 / Net I/σ(I): 22.11 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.55 / Num. unique obs: 2446 / CC1/2: 0.929 / Rpim(I) all: 0.257 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KMP Resolution: 3.2→29.937 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 125.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.937 Å
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Refine LS restraints |
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LS refinement shell |
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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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