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- PDB-6ml2: ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 1) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ml2 | ||||||
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Title | ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 1) | ||||||
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![]() | TRANSCRIPTION/DNA / protein-DNA complex / transcription / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() regulation of immune system process / hematopoietic progenitor cell differentiation / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Cheng, X. / Ren, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of specific DNA binding by the transcription factor ZBTB24. Authors: Ren, R. / Hardikar, S. / Horton, J.R. / Lu, Y. / Zeng, Y. / Singh, A.K. / Lin, K. / Coletta, L.D. / Shen, J. / Lin Kong, C.S. / Hashimoto, H. / Zhang, X. / Chen, T. / Cheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.6 KB | Display | ![]() |
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PDB format | ![]() | 44.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ml3C ![]() 6ml4C ![]() 6ml5C ![]() 6ml6C ![]() 6ml7C ![]() 5v3gS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17274.033 Da / Num. of mol.: 1 / Fragment: zinc fingers 4-8 (UNP residues 375-519) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: DNA chain | Mass: 6143.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#3: DNA chain | Mass: 6125.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2018 |
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→40.12 Å / Num. obs: 36754 / % possible obs: 77.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 699 / CC1/2: 0.864 / Rpim(I) all: 0.264 / % possible all: 27.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5V3G (zinc fingers) + 18-mer B-DNA model Resolution: 1.874→38.232 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.61 / 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: 1.874→38.232 Å
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Refine LS restraints |
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LS refinement shell |
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