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Open data
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Basic information
Entry | Database: PDB / ID: 2evf | ||||||
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Title | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | ||||||
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![]() | CELL CYCLE/DNA / BETA-BARREL / IG-FOLD TRANSCRIPTION FACTOR / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.6 KB | Display | ![]() |
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PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2etwC ![]() 2euvC ![]() 2euwC ![]() 2euxC ![]() 2euzC ![]() 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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 4257.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 1 |
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#2: DNA chain | Mass: 4301.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 2 |
#3: Protein | Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: NDT80 DNA BINDING DOMAIN / Mutation: s146g, i200t 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: 2.32 Å3/Da / Density % sol: 46.9 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 28% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 1 mM DTT. 1:1 Molar ratio protein:DNA, protein at 20mg/ml, 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 / Details: MIRROR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.072158 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→23.56 Å / Num. all: 63123 / Num. obs: 63123 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES Resolution: 1.56→23.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.229 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / 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: 17.392 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→23.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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