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- PDB-2etw: Principles of protein-DNA recognition revealed in the structural ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2etw | ||||||
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Title | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | ||||||
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![]() | CELL CYCLE/DNA / beta sandwich / Ig-fold / B-DNA / CELL CYCLE-DNA COMPLEX | ||||||
Function / homology | ![]() nuclear chromosome / meiotic cell cycle / sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lamoureux, J.S. / Glover, J.N. | ||||||
![]() | ![]() Title: Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes. Authors: Lamoureux, J.S. / Glover, J.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.7 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.7 KB | Display | ![]() |
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Full document | ![]() | 452.9 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2euvC ![]() 2euwC ![]() 2euxC ![]() 2euzC ![]() 2evfC ![]() 2evgC ![]() 2evhC ![]() 2eviC ![]() 2evjC ![]() 1mnnS S: Starting model for refinement C: citing same article ( |
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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
#1: DNA chain | Mass: 4226.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vG1C MSE DNA strand 1 |
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#2: DNA chain | Mass: 4332.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vG1C MSE DNA strand 2 |
#3: Protein | Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: Ndt80 DNA-binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NDT80 / Plasmid: PGEX-6P1 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 1 mM DTT. 10mg/ml protein 1:1 molar ration with duplex DNA , VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072158 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→23.57 Å / Num. all: 51821 / Num. obs: 51821 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.67→1.76 Å / % possible obs: 98.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 7464 / Rsym value: 0.176 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MNN.pdb without water molecules and DNA at position -1,1,2 of the MSE. Resolution: 1.67→23.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.594 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.089 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.272 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→23.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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