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- PDB-7yun: Crystal structure of human BEND6 BEN domain in complex with methy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yun | ||||||
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Title | Crystal structure of human BEND6 BEN domain in complex with methylated DNA | ||||||
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![]() | DNA BINDING PROTEIN / BEND6-DNA complex | ||||||
Function / homology | ![]() negative regulation of Notch signaling pathway / positive regulation of neuron differentiation / transcription corepressor activity / nervous system development / chromatin binding / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, K. / Xiao, Y.Q. / Zhang, J. / Min, J.R. | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yugC ![]() 7yukSC ![]() 7yulC ![]() 8htxC 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: 11806.545 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #3: 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: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M carboxylic acids, 0.1 M imidazole, 0.1 M MES monohydrate (acid) (pH 6.5), 12.5% MPD (v/v), 12.5 % PEG 1000 (v/v), and 12.5% PEG 3350 (w/v). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: May 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→34.34 Å / Num. obs: 15367 / % possible obs: 99.9 % / Redundancy: 4.77 % / Rmerge(I) obs: 0.0559 / Net I/σ(I): 17.36 |
Reflection shell | Resolution: 2.13→2.16 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.2398 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 622 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YUK Resolution: 2.13→34.34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.741 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.344 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→34.34 Å
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Refine LS restraints |
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