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Open data
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Basic information
Entry | Database: PDB / ID: 5zjq | ||||||
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Title | Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence | ||||||
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![]() | TRANSCRIPTION/DNA / AbdB / Exd / DNA / shape / specificity / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() genital disc sexually dimorphic development / male pigmentation / negative regulation of cardioblast cell fate specification / sperm storage / negative regulation of salivary gland boundary specification / specification of segmental identity, abdomen / imaginal disc-derived female genitalia development / determination of genital disc primordium / external genitalia morphogenesis / salivary gland boundary specification ...genital disc sexually dimorphic development / male pigmentation / negative regulation of cardioblast cell fate specification / sperm storage / negative regulation of salivary gland boundary specification / specification of segmental identity, abdomen / imaginal disc-derived female genitalia development / determination of genital disc primordium / external genitalia morphogenesis / salivary gland boundary specification / gonadal mesoderm development / oenocyte development / female genitalia development / open tracheal system development / somatic muscle development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / polytene chromosome band / negative regulation of female receptivity / negative regulation of striated muscle tissue development / neuroendocrine cell differentiation / positive regulation of apoptotic process involved in morphogenesis / segment specification / eye development / regulation of cell fate specification / male genitalia development / germ cell migration / peripheral nervous system development / midgut development / neuron development / cis-regulatory region sequence-specific DNA binding / embryonic organ development / protein-DNA complex / animal organ morphogenesis / transcription coregulator activity / brain development / RNA polymerase II transcription regulator complex / male gonad development / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Baburajendran, N. / Zeiske, T. / Kaczynska, A. / Mann, R. / Honig, B. / Shapiro, L. / Palmer, A.G. | ||||||
![]() | ![]() Title: Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites. Authors: Zeiske, T. / Baburajendran, N. / Kaczynska, A. / Brasch, J. / Palmer, A.G. / Shapiro, L. / Honig, B. / Mann, R.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.6 KB | Display | ![]() |
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PDB format | ![]() | 76.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zjrC ![]() 5zjsC ![]() 5zjtC ![]() 1b8iS 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
#1: Protein | Mass: 10195.751 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 8773.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: DNA chain | Mass: 4263.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: DNA chain | Mass: 4294.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 200mM MgCl2, 0.1M Tris pH 5.8, 17.5% PEG 4000, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.443→29.942 Å / Num. obs: 12413 / % possible obs: 97.33 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 18.49 |
Reflection shell | Resolution: 2.443→2.53 Å / Rmerge(I) obs: 0.539 / Num. unique obs: 980 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B8I Resolution: 2.443→29.942 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.31 Å2 / Biso mean: 45.5612 Å2 / Biso min: 18.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.443→29.942 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: -18.1278 Å / Origin y: 1.8931 Å / Origin z: 119.8547 Å
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Refinement TLS group | Selection details: all |