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Open data
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Basic information
Entry | Database: PDB / ID: 5eg0 | ||||||
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Title | HOXB13-MEIS1 heterodimer bound to DNA | ||||||
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![]() | TRANSCRIPTION / transcription factor / heterodimer / complex / bound to DNA | ||||||
Function / homology | ![]() positive regulation of cardiac muscle myoblast proliferation / epithelial cell maturation involved in prostate gland development / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / methyl-CpG binding / pancreas development / regulation of growth / response to testosterone ...positive regulation of cardiac muscle myoblast proliferation / epithelial cell maturation involved in prostate gland development / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / methyl-CpG binding / pancreas development / regulation of growth / response to testosterone / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / transcription factor binding / epidermis development / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / visual learning / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to wounding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, J. | ||||||
![]() | ![]() Title: Molecular basis of recognition of two distinct DNA sequences by a single transcription factor Authors: Morgunova, E. / Yin, Y. / Jolma, A. / Popov, A. / Taipale, 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 | ![]() | 135 KB | Display | ![]() |
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PDB format | ![]() | 106.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 446.5 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xrmS 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: 6680.738 Da / Num. of mol.: 1 / Fragment: UNP residues 284-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 5586.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 5444.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Protein | Mass: 7411.749 Da / Num. of mol.: 1 / Fragment: UNP residues 217-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 5000, potassium chloride, magnesium chloride, pentanol PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014 |
Radiation | Monochromator: Si(111) and Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→40 Å / Num. obs: 6006 / % possible obs: 99 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.97→3.13 Å / Redundancy: 5 % / Rmerge(I) obs: 2.77 / Mean I/σ(I) obs: 0.4 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XRM Resolution: 3.101→19.946 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.101→19.946 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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