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Open data
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Basic information
Entry | Database: PDB / ID: 7y3k | ||||||
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Title | Structure of SALL4 ZFC4 bound with 16 bp AT-rich dsDNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / SALL4 / zinc finger / AT-rich DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific ...POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / embryonic limb morphogenesis / ventricular septum development / inner cell mass cell proliferation / somatic stem cell population maintenance / heterochromatin / Regulation of PTEN gene transcription / neural tube closure / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ru, W. / Xu, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif. Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C. #1: ![]() Title: Structural studies of SALL family protein zinc finger cluster domains in complex with DNA reveal preferential binding to an AATA tetranucleotide motif Authors: Ru, W. / Koga, T. / Wang, X. / Guo, Q. / Gearhart, M.D. / Zhao, S. / Murphy, M. / Kawakami, H. / Corcoran, D. / Zhang, J. / Zhu, Z. / Yao, X. / Kawakami, Y. / Xu, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.2 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y3iSC ![]() 7y3lC ![]() 7y3mC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 8708.993 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 4896.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 4896.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M BIS-TRIS, pH 5.5, 0.2 M Sodium chloride, 25% polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 8329 / % possible obs: 99.6 % / Redundancy: 10.1 % / CC1/2: 0.969 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 8329 / CC1/2: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7Y3I Resolution: 2.501→28.722 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.99 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.01 Å2 / Biso mean: 59.5261 Å2 / Biso min: 26.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.501→28.722 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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