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Open data
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Basic information
Entry | Database: PDB / ID: 7y3l | ||||||
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Title | Structure of SALL3 ZFC4 bound with 12 bp AT-rich dsDNA | ||||||
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![]() | DNA BINDING PROTEIN/DNA / SALL3 / zinc finger / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / metal ion binding 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 | ![]() | 42.7 KB | Display | ![]() |
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PDB format | ![]() | 24.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y3iSC ![]() 7y3kC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 7645.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: DNA chain | Mass: 3670.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: DNA chain | Mass: 3652.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES monohydrate, pH 6.5, 0.2 M Ammonium sulfate, 30% w/v polyethylene glycol monomethyl ether 5000 |
-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: Oct 7, 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→37.06 Å / Num. obs: 5606 / % possible obs: 98.4 % / Redundancy: 6.1 % / CC1/2: 0.997 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.5→2.6 Å / Num. unique obs: 644 / CC1/2: 0.979 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7Y3I Resolution: 2.5→37.056 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6 / 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: 103.94 Å2 / Biso mean: 39.3404 Å2 / Biso min: 18.32 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→37.056 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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