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- PDB-6dfc: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dfc | ||||||
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Title | Kaiso (ZBTB33) zinc finger DNA binding domain in complex with the specific Kaiso binding sequence (KBS) with a T-to-U substitution | ||||||
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![]() | DNA BINDING PROTEIN/DNA / DNA methylation / Zinc finger / Transcriptional regulator / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences. Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.1 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6df5C ![]() 6df8C ![]() 6df9C ![]() 6dfaC ![]() 6dfbC ![]() 6v8uC ![]() 4f6mS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16217.771 Da / Num. of mol.: 1 / Fragment: residues 471-604 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules DE
#2: DNA chain | Mass: 5452.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 5564.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 3 types, 89 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.2 M Disodium Tartrate, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.02 Å / Num. obs: 36573 / % possible obs: 98.24 % / Redundancy: 9.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0875 / Rrim(I) all: 0.0926 / Net I/σ(I): 17.74 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.84 / Num. unique obs: 3333 / CC1/2: 0.612 / % possible all: 89.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F6M Resolution: 1.85→43.02 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→43.02 Å
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Refine LS restraints |
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LS refinement shell |
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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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