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Open data
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Basic information
Entry | Database: PDB / ID: 4osq | ||||||
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Title | Crystal structure of the S505R mutant of TAL effector dHax3 | ||||||
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![]() | DNA binding protein/DNA / DNA binding protein / DNA / DNA binding protein-DNA complex | ||||||
Function / homology | : / TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, D. / Wu, J.P. / Yan, C.Y. / Pan, X.J. / Yan, N. | ||||||
![]() | ![]() Title: Revisiting the TALE repeat Authors: Deng, D. / Yan, C.Y. / Wu, J.P. / Pan, X.J. / Yan, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 440.5 KB | Display | ![]() |
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PDB format | ![]() | 356.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.1 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 57.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4oshC ![]() 4osiC ![]() 4osjC ![]() 4oskC ![]() 4oslC ![]() 4osmC ![]() 4osrC ![]() 4ossC ![]() 4ostC ![]() 4osvC ![]() 4oswC ![]() 4oszC ![]() 4ot0C ![]() 4ot3C ![]() 4otoC ![]() 3v6tS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51824.625 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720 Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505R,S539G,N572H,S573D,H606N,D607G,N640H,I641D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hax3 / Production host: ![]() ![]() #2: DNA chain | Mass: 5086.280 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 5342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%-15% PEG 3350, 12% ethanol, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. all: 54207 / Num. obs: 54183 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.5 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V6T Resolution: 2.256→32.251 Å / FOM work R set: 0.7927 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 27.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.146 Å2 / ksol: 0.326 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.7 Å2 / Biso mean: 38.03 Å2 / Biso min: 10.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.256→32.251 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.8659 Å / Origin y: 14.2542 Å / Origin z: 24.2953 Å
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Refinement TLS group | Selection details: ALL |