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- PDB-6jtq: RVD HA specifically contacts 5mC through van der Waals interactions -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jtq | |||||||||
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Title | RVD HA specifically contacts 5mC through van der Waals interactions | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / methylation TAL effector / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | : / TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3![]() | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, L. / Yi, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: RVD HA specifically contacts 5mC through van der Waals interactions Authors: Liu, L. / Yi, 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 | ![]() | 228 KB | Display | ![]() |
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PDB format | ![]() | 176.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463 KB | Display | ![]() |
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Full document | ![]() | 488.7 KB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 51876.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 5110.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 5319.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8-10% PEG3350 (w/v), 10% ethanol, 0.1 M MES pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. obs: 39755 / % possible obs: 98.8 % / Redundancy: 3.5 % / Net I/σ(I): 2.03 |
Reflection shell | Resolution: 2.48→2.547 Å |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.039 Å2
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Refinement step | Cycle: 1 / Resolution: 2.48→50 Å
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Refine LS restraints |
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