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Open data
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Basic information
Entry | Database: PDB / ID: 8htx | ||||||
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Title | Crystal structure of BANP in complex with methylated DNA | ||||||
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![]() | DNA BINDING PROTEIN / BANP / BEN Domain | ||||||
Function / homology | ![]() Regulation of TP53 Activity through Association with Co-factors / protein localization to nucleus / negative regulation of protein catabolic process / chromatin organization / nuclear body / cell cycle / DNA binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, J. / Min, J. / Liu, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into DNA recognition by the BEN domain of the transcription factor BANP. Authors: Liu, K. / Zhang, J. / Xiao, Y. / Yang, A. / Song, X. / Li, Y. / Chen, Y. / Hughes, T.R. / Min, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.5 KB | Display | ![]() |
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Full document | ![]() | 467.9 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yugC ![]() 7yukC ![]() 7yulC ![]() 7yunC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16245.380 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3677.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium fluoride, 0.1 M BTP-tris (pH 6.5), 20 % PEG3350 (w/v) |
-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: Dec 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→38.51 Å / Num. obs: 12915 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.995 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1818 / CC1/2: 0.979 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: The solved BANP structure in this study Resolution: 2.8→31.76 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.61 / 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: 2.8→31.76 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.9571 Å / Origin y: 24.8565 Å / Origin z: 12.579 Å
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Refinement TLS group | Selection details: all |